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
129 .getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
130 final static Cursor MOVE_CURSOR = Cursor
131 .getPredefinedCursor( Cursor.MOVE_CURSOR );
132 final static Cursor ARROW_CURSOR = Cursor
133 .getPredefinedCursor( Cursor.DEFAULT_CURSOR );
134 final static Cursor HAND_CURSOR = Cursor
135 .getPredefinedCursor( Cursor.HAND_CURSOR );
136 final static Cursor WAIT_CURSOR = Cursor
137 .getPredefinedCursor( Cursor.WAIT_CURSOR );
138 private final static long serialVersionUID = -978349745916505029L;
139 private final static int EURO_D = 10;
140 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
141 private final static int MIN_ROOT_LENGTH = 3;
142 private final static int BOX_SIZE = 4;
143 private final static int HALF_BOX_SIZE = TreePanel.BOX_SIZE / 2;
144 private final static int MAX_SUBTREES = 100;
145 private final static int MAX_NODE_FRAMES = 10;
146 private final static int MOVE = 20;
147 private final static NumberFormat FORMATTER_CONFIDENCE;
148 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
149 private final static int WIGGLE = 2;
150 private final static int HALF_BOX_SIZE_PLUS_WIGGLE = HALF_BOX_SIZE + WIGGLE;
151 private final static int LIMIT_FOR_HQ_RENDERING = 1000;
152 // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not
153 // being static anymore (02/20/2009).
154 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
155 RenderingHints.VALUE_RENDER_DEFAULT );
156 private File _treefile = null;
157 private Configuration _configuration = null;
158 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
159 private int _node_frame_index = 0;
160 private Phylogeny _phylogeny = null;
161 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
162 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
163 private int _subtree_index = 0;
164 private MainPanel _main_panel = null;
165 private Set<Integer> _found_nodes = null;
166 private PhylogenyNode _highlight_node = null;
167 private JPopupMenu _node_popup_menu = null;
168 private JMenuItem _node_popup_menu_items[] = null;
169 private int _longest_ext_node_info = 0;
170 private float _x_correction_factor = 0.0f;
171 private float _ov_x_correction_factor = 0.0f;
172 private float _x_distance = 0.0f;
173 private float _y_distance = 0.0f;
174 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
175 private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
176 private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
177 private float _last_drag_point_x = 0;
178 private float _last_drag_point_y = 0;
179 private ControlPanel _control_panel = null;
180 private int _external_node_index = 0;
181 private final Polygon _polygon = new Polygon();
182 private final StringBuilder _sb = new StringBuilder();
183 private JColorChooser _color_chooser = null;
184 private double _scale_distance = 0.0;
185 private String _scale_label = null;
186 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
187 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
188 private final Line2D _line = new Line2D.Float();
189 private final Ellipse2D _ellipse = new Ellipse2D.Float();
190 private final Rectangle2D _rectangle = new Rectangle2D.Float();
191 private Options _options = null;
192 private float _ov_max_width = 0;
193 private float _ov_max_height = 0;
194 private int _ov_x_position = 0;
195 private int _ov_y_position = 0;
196 private int _ov_y_start = 0;
197 private float _ov_y_distance = 0;
198 private float _ov_x_distance = 0;
199 private boolean _ov_on = false;
200 private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
201 private float _urt_factor = 1;
202 private float _urt_factor_ov = 1;
203 private final boolean _phy_has_branch_lengths;
204 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
205 private boolean _in_ov_rect = false;
206 private boolean _in_ov = false;
207 private final Rectangle _ov_virtual_rectangle = new Rectangle();
208 final private static double _180_OVER_PI = 180.0 / Math.PI;
209 private static final float ROUNDED_D = 8;
210 private int _circ_max_depth;
211 private int _circ_num_ext_nodes;
212 private PhylogenyNode _root;
213 final private Arc2D _arc = new Arc2D.Double();
214 final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
215 final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
216 HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
217 private AffineTransform _at;
218 private double _max_distance_to_root = -1;
219 private int _dynamic_hiding_factor = 0;
220 private boolean _edited = false;
221 private Popup _node_desc_popup;
222 private JTextArea _rollover_popup;
223 //private final short _skip_counter = 0;
224 private final StringBuffer _popup_buffer = new StringBuffer();
225 final private static Font POPUP_FONT = new Font( Configuration
226 .getDefaultFontFamilyName(),
229 private static final boolean DRAW_MEAN_COUNTS = true; //TODO remove me later
230 private Sequence _query_sequence = null;
231 private final FontRenderContext _frc = new FontRenderContext( null,
234 // expression values menu:
235 private DescriptiveStatistics _statistics_for_vector_data;
236 // private Image offscreenImage;
237 // private Graphics offscreenGraphics;
238 // private Dimension offscreenDimension;
240 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
241 dfs.setDecimalSeparator( '.' );
242 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
243 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
246 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
247 requestFocusInWindow();
248 addKeyListener( new KeyAdapter() {
251 public void keyPressed( final KeyEvent key_event ) {
252 keyPressedCalls( key_event );
253 requestFocusInWindow();
256 addFocusListener( new FocusAdapter() {
259 public void focusGained( final FocusEvent e ) {
260 requestFocusInWindow();
263 if ( ( t == null ) || t.isEmpty() ) {
264 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
266 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
268 _configuration = configuration;
270 _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
272 // if ( !_phylogeny.isEmpty() ) {
273 _phylogeny.recalculateNumberOfExternalDescendants( true );
274 checkForVectorProperties( _phylogeny );
276 setBackground( getTreeColorSet().getBackgroundColor() );
277 final MouseListener mouse_listener = new MouseListener( this );
278 addMouseListener( mouse_listener );
279 addMouseMotionListener( mouse_listener );
280 addMouseWheelListener( this );
281 calculateScaleDistance();
282 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
283 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
284 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
287 public void checkForVectorProperties( final Phylogeny phy ) {
288 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
289 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
290 final PhylogenyNode node = iter.next();
291 if ( node.getNodeData().getProperties() != null ) {
292 final PropertiesMap pm = node.getNodeData().getProperties();
293 final double[] vector = new double[ pm.getProperties().size() ];
295 for( final String ref : pm.getProperties().keySet() ) {
296 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
297 final Property p = pm.getProperty( ref );
298 final String value_str = p.getValue();
299 final String index_str = ref
300 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
303 d = Double.parseDouble( value_str );
305 catch ( final NumberFormatException e ) {
306 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
307 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
312 i = Integer.parseInt( index_str );
314 catch ( final NumberFormatException e ) {
315 JOptionPane.showMessageDialog( this,
316 "Could not parse \"" + index_str
317 + "\" into index for vector data",
318 "Problem with Vector Data",
319 JOptionPane.ERROR_MESSAGE );
323 JOptionPane.showMessageDialog( this,
324 "Attempt to use negative index for vector data",
325 "Problem with Vector Data",
326 JOptionPane.ERROR_MESSAGE );
334 final List<Double> vector_l = new ArrayList<Double>( counter );
335 for( int i = 0; i < counter; ++i ) {
336 vector_l.add( vector[ i ] );
338 node.getNodeData().setVector( vector_l );
341 if ( stats.getN() > 0 ) {
342 _statistics_for_vector_data = stats;
346 final public void actionPerformed( final ActionEvent e ) {
348 boolean done = false;
349 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
350 for( index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
351 // NOTE: index corresponds to the indices of click-to options
352 // in the control panel.
353 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
354 // Set this as the new default click-to action
355 _main_panel.getControlPanel().setClickToAction( index );
356 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
357 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
358 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
363 requestFocusInWindow();
366 final private void addEmptyNode( final PhylogenyNode node ) {
367 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
368 errorMessageNoCutCopyPasteInUnrootedDisplay();
371 final String label = getASimpleTextRepresentationOfANode( node );
373 if ( ForesterUtil.isEmpty( label ) ) {
374 msg = "How to add the new, empty node?";
377 msg = "How to add the new, empty node to node" + label + "?";
379 final Object[] options = { "As sibling", "As descendant", "Cancel" };
380 final int r = JOptionPane.showOptionDialog( this,
382 "Addition of Empty New Node",
383 JOptionPane.CLOSED_OPTION,
384 JOptionPane.QUESTION_MESSAGE,
388 boolean add_as_sibling = true;
390 add_as_sibling = false;
395 final Phylogeny phy = new Phylogeny();
396 phy.setRoot( new PhylogenyNode() );
397 phy.setRooted( true );
398 if ( add_as_sibling ) {
399 if ( node.isRoot() ) {
400 JOptionPane.showMessageDialog( this,
401 "Cannot add sibling to root",
402 "Attempt to add sibling to root",
403 JOptionPane.ERROR_MESSAGE );
406 phy.addAsSibling( node );
409 phy.addAsChild( node );
411 _phylogeny.externalNodesHaveChanged();
412 _phylogeny.hashIDs();
413 _phylogeny.recalculateNumberOfExternalDescendants( true );
414 resetNodeIdToDistToLeafMap();
419 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
420 final boolean is_vertical,
422 final boolean to_pdf,
423 final boolean to_graphics_file ) {
424 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
425 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
426 g.setColor( Color.BLACK );
428 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
429 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
430 && ( getCutOrCopiedTree() != null )
431 && ( getCopiedAndPastedNodes() != null )
433 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
434 g.setColor( getTreeColorSet().getFoundColor() );
436 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
437 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
440 g.setColor( getTreeColorSet().getBranchColorForPdf() );
443 g.setColor( getTreeColorSet().getBranchColor() );
447 final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) {
448 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
449 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
452 g.setColor( getTreeColorSet().getBranchColor() );
456 final private void blast( final PhylogenyNode node ) {
457 if ( !isCanBlast( node ) ) {
458 JOptionPane.showMessageDialog( this,
459 "No sequence information present",
461 JOptionPane.WARNING_MESSAGE );
464 if ( node.getNodeData().isHasSequence() ) {
466 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
467 name = node.getNodeData().getSequence().getName();
469 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
470 name = node.getNodeData().getSequence().getSymbol();
472 else if ( node.getNodeData().getSequence().getAccession() != null ) {
473 name = node.getNodeData().getSequence().getAccession().getValue();
475 if ( !ForesterUtil.isEmpty( name ) ) {
477 System.out.println( "trying: " + name );
478 final Blast s = new Blast();
481 catch ( final Exception e ) {
488 final void calcMaxDepth() {
489 if ( _phylogeny != null ) {
490 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
495 * Calculate the length of the distance between the given node and its
501 * @return the distance value
503 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
504 if ( getControlPanel().isDrawPhylogram() ) {
505 if ( node.getDistanceToParent() < 0.0 ) {
508 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
511 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
512 return getXdistance();
514 return getXdistance() * factor;
518 final private Color calculateColorForAnnotation( final PhylogenyData ann ) {
519 Color c = getTreeColorSet().getAnnotationColor();
520 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
521 c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() );
523 c = getTreeColorSet().getAnnotationColor();
529 final void calculateLongestExtNodeInfo() {
530 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
534 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
536 if ( node.isCollapse() ) {
539 if ( getControlPanel().isShowNodeNames() ) {
540 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
542 if ( node.getNodeData().isHasSequence() ) {
543 if ( getControlPanel().isShowSequenceAcc()
544 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
545 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
549 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
550 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
552 if ( getControlPanel().isShowGeneSymbols()
553 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
554 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
556 if ( getControlPanel().isShowAnnotation()
557 && ( node.getNodeData().getSequence().getAnnotations() != null )
558 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
559 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
564 if ( node.getNodeData().isHasTaxonomy() ) {
565 final Taxonomy tax = node.getNodeData().getTaxonomy();
566 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
567 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
569 if ( getControlPanel().isShowTaxonomyScientificNames()
570 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
571 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
573 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
574 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
577 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
578 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
579 .getGainedCharactersAsStringBuffer().toString() );
581 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
582 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
583 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
584 .getRenderingSize().getWidth();
586 if ( sum >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
587 setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
590 if ( sum > longest ) {
594 if ( longest >= Constants.EXT_NODE_INFO_LENGTH_MAX ) {
595 setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX );
598 setLongestExtNodeInfo( longest );
602 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
603 if ( getControlPanel().isDrawPhylogram() ) {
604 if ( node.getDistanceToParent() < 0.0 ) {
607 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
610 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
611 return getOvXDistance();
613 return getOvXDistance() * factor;
617 final void calculateScaleDistance() {
618 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
621 final double height = getMaxDistanceToRoot();
623 if ( ( height <= 0.5 ) ) {
624 setScaleDistance( 0.01 );
626 else if ( height <= 5.0 ) {
627 setScaleDistance( 0.1 );
629 else if ( height <= 50.0 ) {
630 setScaleDistance( 1 );
632 else if ( height <= 500.0 ) {
633 setScaleDistance( 10 );
636 setScaleDistance( 100 );
640 setScaleDistance( 0.0 );
642 String scale_label = String.valueOf( getScaleDistance() );
643 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
644 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
646 setScaleLabel( scale_label );
649 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
650 String species = tax.getTaxonomyCode();
651 if ( ForesterUtil.isEmpty( species ) ) {
652 species = tax.getScientificName();
653 if ( ForesterUtil.isEmpty( species ) ) {
654 species = tax.getCommonName();
657 if ( ForesterUtil.isEmpty( species ) ) {
658 return getTreeColorSet().getTaxonomyColor();
660 // Look in species hash
661 Color c = getControlPanel().getSpeciesColors().get( species );
663 c = Util.calculateColorFromString( species );
664 getControlPanel().getSpeciesColors().put( species, c );
669 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
670 JOptionPane.showMessageDialog( this,
671 "Cannot launch web browser for " + type_type + " data of this node",
672 "Cannot launch web browser",
673 JOptionPane.WARNING_MESSAGE );
677 * Collapse the tree from the given node
682 final void collapse( final PhylogenyNode node ) {
683 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
684 JOptionPane.showMessageDialog( this,
685 "Cannot collapse in unrooted display type",
686 "Attempt to collapse in unrooted display",
687 JOptionPane.WARNING_MESSAGE );
690 if ( !node.isExternal() && !node.isRoot() ) {
691 final boolean collapse = !node.isCollapse();
692 Util.collapseSubtree( node, collapse );
693 _phylogeny.recalculateNumberOfExternalDescendants( true );
694 resetNodeIdToDistToLeafMap();
695 calculateLongestExtNodeInfo();
696 resetPreferredSize();
698 _main_panel.adjustJScrollPane();
703 final void collapseSpeciesSpecificSubtrees() {
704 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
708 Util.collapseSpeciesSpecificSubtrees( _phylogeny );
709 _phylogeny.recalculateNumberOfExternalDescendants( true );
710 resetNodeIdToDistToLeafMap();
711 calculateLongestExtNodeInfo();
712 resetPreferredSize();
713 _main_panel.adjustJScrollPane();
718 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
719 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
720 JOptionPane.showMessageDialog( this,
721 "Cannot colorize subtree in unrooted display type",
722 "Attempt to colorize subtree in unrooted display",
723 JOptionPane.WARNING_MESSAGE );
726 _control_panel.setColorBranches( true );
727 if ( _control_panel.getColorBranchesCb() != null ) {
728 _control_panel.getColorBranchesCb().setSelected( true );
730 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
731 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
736 final private void colorSubtree( final PhylogenyNode node ) {
737 Color intitial_color = null;
738 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
739 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
740 intitial_color = PhylogenyMethods.getBranchColorValue( node );
743 intitial_color = getTreeColorSet().getBranchColor();
745 _color_chooser.setColor( intitial_color );
746 _color_chooser.setPreviewPanel( new JPanel() );
747 final JDialog dialog = JColorChooser
749 "Subtree colorization",
752 new SubtreeColorizationActionListener( _color_chooser, node ),
754 dialog.setVisible( true );
757 final void confColor() {
758 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
762 Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
763 _control_panel.setColorBranches( true );
764 if ( _control_panel.getColorBranchesCb() != null ) {
765 _control_panel.getColorBranchesCb().setSelected( true );
771 final private void copySubtree( final PhylogenyNode node ) {
772 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
773 errorMessageNoCutCopyPasteInUnrootedDisplay();
776 setCutOrCopiedTree( _phylogeny.copy( node ) );
777 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
778 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
779 for( final PhylogenyNode n : nodes ) {
780 node_ids.add( n.getId() );
782 node_ids.add( node.getId() );
783 setCopiedAndPastedNodes( node_ids );
787 final private void cutSubtree( final PhylogenyNode node ) {
788 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
789 errorMessageNoCutCopyPasteInUnrootedDisplay();
792 if ( node.isRoot() ) {
793 JOptionPane.showMessageDialog( this,
794 "Cannot cut entire tree as subtree",
795 "Attempt to cut entire tree",
796 JOptionPane.ERROR_MESSAGE );
799 final String label = getASimpleTextRepresentationOfANode( node );
800 final int r = JOptionPane.showConfirmDialog( null,
801 "Cut subtree" + label + "?",
802 "Confirm Cutting of Subtree",
803 JOptionPane.YES_NO_OPTION );
804 if ( r != JOptionPane.OK_OPTION ) {
807 setCopiedAndPastedNodes( null );
808 setCutOrCopiedTree( _phylogeny.copy( node ) );
809 _phylogeny.deleteSubtree( node, true );
810 _phylogeny.hashIDs();
811 _phylogeny.recalculateNumberOfExternalDescendants( true );
812 resetNodeIdToDistToLeafMap();
817 final private void cycleColors() {
818 getMainPanel().getTreeColorSet().cycleColorScheme();
819 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
820 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
824 final void decreaseDomainStructureEvalueThreshold() {
825 if ( _domain_structure_e_value_thr_exp > -20 ) {
826 _domain_structure_e_value_thr_exp -= 1;
830 final private void decreaseOvSize() {
831 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
832 setOvMaxWidth( getOvMaxWidth() - 5 );
833 setOvMaxHeight( getOvMaxHeight() - 5 );
835 getControlPanel().displayedPhylogenyMightHaveChanged( false );
839 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
840 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
841 errorMessageNoCutCopyPasteInUnrootedDisplay();
844 if ( node.isRoot() ) {
845 JOptionPane.showMessageDialog( this,
846 "Cannot delete entire tree",
847 "Attempt to delete entire tree",
848 JOptionPane.ERROR_MESSAGE );
851 final String label = getASimpleTextRepresentationOfANode( node );
852 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
853 final int r = JOptionPane.showOptionDialog( this,
854 "Delete" + label + "?",
855 "Delete Node/Subtree",
856 JOptionPane.CLOSED_OPTION,
857 JOptionPane.QUESTION_MESSAGE,
861 boolean node_only = true;
869 PhylogenyMethods.removeNode( node, _phylogeny );
872 _phylogeny.deleteSubtree( node, true );
874 _phylogeny.externalNodesHaveChanged();
875 _phylogeny.hashIDs();
876 _phylogeny.recalculateNumberOfExternalDescendants( true );
877 resetNodeIdToDistToLeafMap();
882 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
883 makePopupMenus( node );
884 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
885 _node_popup_menu.show( this, x, y );
888 final private void drawArc( final double x,
892 final double start_angle,
893 final double arc_angle,
894 final Graphics2D g ) {
895 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
899 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
900 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
903 _line.setLine( x1, y1, x2, y2 );
907 final private void drawOval( final double x,
911 final Graphics2D g ) {
912 _ellipse.setFrame( x, y, width, heigth );
916 final private void drawOvalFilled( final double x,
920 final Graphics2D g ) {
921 _ellipse.setFrame( x, y, width, heigth );
925 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
926 _rectangle.setFrame( x, y, width, heigth );
927 g.draw( _rectangle );
930 final private void drawRectFilled( final double x,
934 final Graphics2D g ) {
935 _rectangle.setFrame( x, y, width, heigth );
936 g.fill( _rectangle );
939 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
940 JOptionPane.showMessageDialog( this,
941 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
942 "Attempt to cut/copy/paste/add/delete in unrooted display",
943 JOptionPane.ERROR_MESSAGE );
947 * Find the node, if any, at the given location
951 * @return pointer to the node at x,y, null if not found
953 final PhylogenyNode findNode( final int x, final int y ) {
954 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
957 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
958 final PhylogenyNode node = iter.next();
959 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
960 && ( ( node.getXcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= x )
961 && ( ( node.getXcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= x )
962 && ( ( node.getYcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= y )
963 && ( ( node.getYcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= y ) ) {
970 final private String getASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
971 final String tax = PhylogenyMethods.getSpecies( node );
972 String label = node.getName();
973 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
974 label = label + " " + tax;
976 else if ( !ForesterUtil.isEmpty( tax ) ) {
982 if ( !ForesterUtil.isEmpty( label ) ) {
983 label = " [" + label + "]";
988 final Configuration getConfiguration() {
989 return _configuration;
992 final ControlPanel getControlPanel() {
993 return _control_panel;
996 final private Set<Integer> getCopiedAndPastedNodes() {
997 return getMainPanel().getCopiedAndPastedNodes();
1000 final private Phylogeny getCutOrCopiedTree() {
1001 return getMainPanel().getCutOrCopiedTree();
1004 final int getDomainStructureEvalueThreshold() {
1005 return _domain_structure_e_value_thr_exp;
1008 final Set<Integer> getFoundNodes() {
1009 return _found_nodes;
1012 final private float getLastDragPointX() {
1013 return _last_drag_point_x;
1016 final private float getLastDragPointY() {
1017 return _last_drag_point_y;
1020 final int getLongestExtNodeInfo() {
1021 return _longest_ext_node_info;
1024 final public MainPanel getMainPanel() {
1028 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
1029 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
1030 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
1031 _nodeid_dist_to_leaf.put( node.getId(), m );
1035 return _nodeid_dist_to_leaf.get( node.getId() );
1039 final private double getMaxDistanceToRoot() {
1040 if ( _max_distance_to_root < 0 ) {
1041 recalculateMaxDistanceToRoot();
1043 return _max_distance_to_root;
1046 final Options getOptions() {
1047 if ( _options == null ) {
1048 _options = getControlPanel().getOptions();
1053 final private float getOvMaxHeight() {
1054 return _ov_max_height;
1057 final private float getOvMaxWidth() {
1058 return _ov_max_width;
1061 final Rectangle2D getOvRectangle() {
1062 return _ov_rectangle;
1065 final Rectangle getOvVirtualRectangle() {
1066 return _ov_virtual_rectangle;
1069 final private float getOvXcorrectionFactor() {
1070 return _ov_x_correction_factor;
1073 final private float getOvXDistance() {
1074 return _ov_x_distance;
1077 final private int getOvXPosition() {
1078 return _ov_x_position;
1081 final private float getOvYDistance() {
1082 return _ov_y_distance;
1085 final private int getOvYPosition() {
1086 return _ov_y_position;
1089 final private int getOvYStart() {
1094 * Get a pointer to the phylogeny
1096 * @return a pointer to the phylogeny
1098 final Phylogeny getPhylogeny() {
1102 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
1103 return _graphics_type;
1106 final private double getScaleDistance() {
1107 return _scale_distance;
1110 final private String getScaleLabel() {
1111 return _scale_label;
1114 final double getStartingAngle() {
1115 return _urt_starting_angle;
1119 * Find a color for this species name.
1122 * @return the species color
1124 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
1125 if ( node.getNodeData().isHasTaxonomy() ) {
1126 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
1128 // return non-colorized color
1129 return getTreeColorSet().getTaxonomyColor();
1133 * @return pointer to colorset for tree drawing
1135 final TreeColorSet getTreeColorSet() {
1136 return getMainPanel().getTreeColorSet();
1139 final File getTreeFile() {
1143 final private TreeFontSet getTreeFontSet() {
1144 return getMainPanel().getTreeFontSet();
1147 final private float getUrtFactor() {
1151 final private float getUrtFactorOv() {
1152 return _urt_factor_ov;
1155 final float getXcorrectionFactor() {
1156 return _x_correction_factor;
1159 final float getXdistance() {
1163 final float getYdistance() {
1167 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
1170 showNodeFrame( node );
1185 colorSubtree( node );
1200 copySubtree( node );
1203 pasteSubtree( node );
1205 case DELETE_NODE_OR_SUBTREE:
1206 deleteNodeOrSubtree( node );
1209 addEmptyNode( node );
1211 case EDIT_NODE_DATA:
1212 showNodeEditFrame( node );
1215 throw new IllegalArgumentException( "unknown action: " + action );
1219 final void increaseDomainStructureEvalueThreshold() {
1220 if ( _domain_structure_e_value_thr_exp < 3 ) {
1221 _domain_structure_e_value_thr_exp += 1;
1225 final private void increaseOvSize() {
1226 if ( ( getOvMaxWidth() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 )
1227 && ( getOvMaxHeight() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
1228 .getHeight() / 2 ) ) {
1229 setOvMaxWidth( getOvMaxWidth() + 5 );
1230 setOvMaxHeight( getOvMaxHeight() + 5 );
1232 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1236 final void inferCommonPartOfScientificNames() {
1237 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1241 Util.inferCommonPartOfScientificNames( _phylogeny );
1246 final private void init() {
1247 _color_chooser = new JColorChooser();
1248 _rollover_popup = new JTextArea();
1249 _rollover_popup.setFont( POPUP_FONT );
1250 resetNodeIdToDistToLeafMap();
1252 setTreeFile( null );
1254 initializeOvSettings();
1255 setStartingAngle( TWO_PI * 3 / 4 );
1256 final ImageLoader il = new ImageLoader( this );
1257 new Thread( il ).start();
1260 final private void initializeOvSettings() {
1261 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
1262 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
1265 final void initNodeData() {
1266 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1269 double max_original_domain_structure_width = 0.0;
1270 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1271 if ( node.getNodeData().isHasSequence()
1272 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1273 RenderableDomainArchitecture rds = null;
1274 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1275 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1276 getConfiguration() );
1277 node.getNodeData().getSequence().setDomainArchitecture( rds );
1280 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1282 if ( getControlPanel().isShowDomainArchitectures() ) {
1283 final double dsw = rds.getOriginalSize().getWidth();
1284 if ( dsw > max_original_domain_structure_width ) {
1285 max_original_domain_structure_width = dsw;
1290 if ( getControlPanel().isShowDomainArchitectures() ) {
1291 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1292 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1293 if ( node.getNodeData().isHasSequence()
1294 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1295 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1296 .getSequence().getDomainArchitecture();
1297 rds.setRenderingFactorWidth( ds_factor_width );
1298 rds.setParameter( _domain_structure_e_value_thr_exp );
1304 final boolean inOv( final MouseEvent e ) {
1305 return ( ( e.getX() > getVisibleRect().x + getOvXPosition() + 1 )
1306 && ( e.getX() < getVisibleRect().x + getOvXPosition() + getOvMaxWidth() - 1 )
1307 && ( e.getY() > getVisibleRect().y + getOvYPosition() + 1 ) && ( e.getY() < getVisibleRect().y
1308 + getOvYPosition() + getOvMaxHeight() - 1 ) );
1311 final boolean inOvRectangle( final MouseEvent e ) {
1312 return ( ( e.getX() >= getOvRectangle().getX() - 1 )
1313 && ( e.getX() <= getOvRectangle().getX() + getOvRectangle().getWidth() + 1 )
1314 && ( e.getY() >= getOvRectangle().getY() - 1 ) && ( e.getY() <= getOvRectangle().getY()
1315 + getOvRectangle().getHeight() + 1 ) );
1318 final private boolean inOvVirtualRectangle( final int x, final int y ) {
1319 return ( ( x >= getOvVirtualRectangle().x - 1 )
1320 && ( x <= getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 )
1321 && ( y >= getOvVirtualRectangle().y - 1 ) && ( y <= getOvVirtualRectangle().y
1322 + getOvVirtualRectangle().height + 1 ) );
1325 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
1326 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
1329 final boolean isApplet() {
1330 return getMainPanel() instanceof MainPanelApplets;
1333 final private boolean isCanBlast( final PhylogenyNode node ) {
1334 return ( node.getNodeData().isHasSequence() && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil
1335 .isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) )
1336 || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil.isEmpty( node
1337 .getNodeData().getSequence().getSymbol() ) ) );
1340 final boolean isCanCollapse() {
1341 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1344 final boolean isCanColorSubtree() {
1345 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1348 final boolean isCanCopy() {
1349 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1352 final boolean isCanCut( final PhylogenyNode node ) {
1353 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1357 final boolean isCanDelete() {
1358 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1361 final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
1362 if ( node.getNodeData().isHasSequence()
1363 && ( node.getNodeData().getSequence().getAccession() != null )
1364 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
1365 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
1366 && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
1367 .toLowerCase() ) ) {
1373 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
1374 if ( node.getNodeData().isHasTaxonomy()
1375 && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
1376 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
1377 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
1378 .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
1379 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
1380 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
1381 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
1382 .getNodeData().getTaxonomy().getIdentifier() != null )
1383 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
1384 .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
1392 final boolean isCanPaste() {
1393 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1394 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1397 final boolean isCanReroot() {
1398 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1401 final boolean isCanSubtree( final PhylogenyNode node ) {
1402 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1403 .isRoot() || ( _subtree_index > 0 ) ) );
1406 final boolean isEdited() {
1410 final private boolean isInFoundNodes( final PhylogenyNode node ) {
1411 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
1414 final private boolean isInOv() {
1418 final boolean isInOvRect() {
1422 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
1424 if ( getControlPanel().isShowTaxonomyImages() ) {
1425 y_dist = 40 + ( int ) getYdistance();
1427 return ( ( node.getYcoord() < getVisibleRect().getMinY() - y_dist )
1428 || ( node.getYcoord() > getVisibleRect().getMaxY() + y_dist ) || ( ( node.getParent() != null ) && ( node
1429 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
1432 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
1433 return ( ( node.getYcoord() < getVisibleRect().getMinY() - 20 )
1434 || ( node.getYcoord() > getVisibleRect().getMaxY() + 20 )
1435 || ( node.getXcoord() < getVisibleRect().getMinX() - 20 ) || ( node.getXcoord() > getVisibleRect()
1436 .getMaxX() + 20 ) );
1439 final private boolean isNonLinedUpCladogram() {
1440 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
1443 final boolean isOvOn() {
1447 final boolean isPhyHasBranchLengths() {
1448 return _phy_has_branch_lengths;
1451 final private boolean isUniformBranchLengthsForCladogram() {
1452 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
1455 final private void keyPressedCalls( final KeyEvent e ) {
1456 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
1457 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
1458 if ( !isInOvRect() ) {
1459 setInOvRect( true );
1462 else if ( isInOvRect() ) {
1463 setInOvRect( false );
1466 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
1467 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1468 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
1469 getMainPanel().getTreeFontSet().mediumFonts();
1470 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1472 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1473 getMainPanel().getTreeFontSet().decreaseFontSize();
1474 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1476 else if ( plusPressed( e.getKeyCode() ) ) {
1477 getMainPanel().getTreeFontSet().increaseFontSize();
1478 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1482 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1483 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
1484 getControlPanel().showWhole();
1486 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
1487 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
1488 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
1489 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
1490 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1491 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1493 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1494 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1495 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1497 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1498 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1499 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1500 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1502 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1503 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1504 Constants.WHEEL_ZOOM_IN_FACTOR );
1505 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1512 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1515 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1519 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1523 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1524 scroll_position.x = scroll_position.x + dx;
1525 scroll_position.y = scroll_position.y + dy;
1526 if ( scroll_position.x <= 0 ) {
1527 scroll_position.x = 0;
1530 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1531 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1532 if ( scroll_position.x >= max_x ) {
1533 scroll_position.x = max_x;
1536 if ( scroll_position.y <= 0 ) {
1537 scroll_position.y = 0;
1540 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1541 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1542 if ( scroll_position.y >= max_y ) {
1543 scroll_position.y = max_y;
1547 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1550 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1551 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1552 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1553 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1554 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1556 else if ( plusPressed( e.getKeyCode() ) ) {
1557 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1558 Constants.WHEEL_ZOOM_IN_FACTOR );
1559 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1560 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1562 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
1563 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1564 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1565 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
1566 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1569 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
1570 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1571 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1572 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
1573 if ( getStartingAngle() < 0 ) {
1574 setStartingAngle( TWO_PI + getStartingAngle() );
1576 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1579 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
1580 boolean selected = false;
1581 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
1582 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1586 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1588 if ( getMainPanel().getMainFrame() == null ) {
1589 // Must be "E" applet version.
1590 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1591 if ( ae.getlabelDirectionCbmi() != null ) {
1592 ae.getlabelDirectionCbmi().setSelected( selected );
1596 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
1600 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
1601 switchDisplaygetPhylogenyGraphicsType();
1604 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
1608 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
1609 MainFrame.cycleOverview( getOptions(), this );
1612 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
1615 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
1622 final private void makePopupMenus( final PhylogenyNode node ) {
1623 _node_popup_menu = new JPopupMenu();
1624 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
1625 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
1626 for( int i = 0; i < clickto_names.size(); i++ ) {
1627 final String title = clickto_names.get( i );
1628 _node_popup_menu_items[ i ] = new JMenuItem( title );
1629 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
1630 _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
1632 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
1633 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
1635 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
1636 if ( Constants.__RELEASE || Constants.__SNAPSHOT_RELEASE ) {
1639 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
1641 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
1642 if ( !getOptions().isEditable() ) {
1645 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
1647 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
1648 if ( !getOptions().isEditable() ) {
1651 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
1653 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
1654 if ( !getOptions().isEditable() ) {
1657 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
1659 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
1660 if ( !getOptions().isEditable() ) {
1663 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
1665 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
1666 if ( !getOptions().isEditable() ) {
1670 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
1671 if ( !getOptions().isEditable() ) {
1675 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
1676 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
1678 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
1679 _node_popup_menu_items[ i ].setEnabled( isCanCollapse() );
1681 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
1682 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
1684 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
1685 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
1687 _node_popup_menu_items[ i ].addActionListener( this );
1688 _node_popup_menu.add( _node_popup_menu_items[ i ] );
1692 final void midpointRoot() {
1693 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1696 if ( !_phylogeny.isRerootable() ) {
1697 JOptionPane.showMessageDialog( this,
1698 "This is not rerootable",
1700 JOptionPane.WARNING_MESSAGE );
1704 PhylogenyMethods.midpointRoot( _phylogeny );
1705 resetNodeIdToDistToLeafMap();
1710 final void mouseClicked( final MouseEvent e ) {
1711 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1712 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1713 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1714 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - getOvRectangle().getWidth() / 2.0 )
1716 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - getOvRectangle().getHeight() / 2.0 )
1724 final double max_x = getWidth() - getVisibleRect().width;
1725 final double max_y = getHeight() - getVisibleRect().height;
1732 getMainPanel().getCurrentScrollPane().getViewport()
1733 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1734 setInOvRect( true );
1738 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1739 if ( node != null ) {
1740 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1743 _highlight_node = node;
1744 // Check if shift key is down
1745 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1746 // Yes, so add to _found_nodes
1747 if ( getFoundNodes() == null ) {
1748 setFoundNodes( new HashSet<Integer>() );
1750 getFoundNodes().add( node.getId() );
1751 // Check if control key is down
1753 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1754 // Yes, so pop-up menu
1755 displayNodePopupMenu( node, e.getX(), e.getY() );
1756 // Handle unadorned click
1759 // Check for right mouse button
1760 if ( e.getModifiers() == 4 ) {
1761 displayNodePopupMenu( node, e.getX(), e.getY() );
1764 // if not in _found_nodes, clear _found_nodes
1765 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1770 // no node was clicked
1771 _highlight_node = null;
1777 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1778 setCursor( MOVE_CURSOR );
1779 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1780 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1781 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1782 if ( scroll_position.x < 0 ) {
1783 scroll_position.x = 0;
1786 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1787 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1788 if ( scroll_position.x > max_x ) {
1789 scroll_position.x = max_x;
1792 if ( scroll_position.y < 0 ) {
1793 scroll_position.y = 0;
1796 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1797 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1798 if ( scroll_position.y > max_y ) {
1799 scroll_position.y = max_y;
1802 if ( isOvOn() || getOptions().isShowScale() ) {
1805 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1808 final void mouseDragInOvRectangle( final MouseEvent e ) {
1809 setCursor( HAND_CURSOR );
1810 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1811 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1812 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1813 double dx = ( w_ratio * e.getX() - w_ratio * getLastDragPointX() );
1814 double dy = ( h_ratio * e.getY() - h_ratio * getLastDragPointY() );
1815 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1816 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1817 if ( scroll_position.x <= 0 ) {
1818 scroll_position.x = 0;
1822 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1823 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1824 if ( scroll_position.x >= max_x ) {
1826 scroll_position.x = max_x;
1829 if ( scroll_position.y <= 0 ) {
1831 scroll_position.y = 0;
1834 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1835 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1836 if ( scroll_position.y >= max_y ) {
1838 scroll_position.y = max_y;
1842 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1843 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1844 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1847 final void mouseMoved( final MouseEvent e ) {
1848 requestFocusInWindow();
1849 if ( getControlPanel().isNodeDescPopup() ) {
1850 if ( _node_desc_popup != null ) {
1851 _node_desc_popup.hide();
1852 _node_desc_popup = null;
1855 if ( getOptions().isShowOverview() && isOvOn() ) {
1856 if ( inOvVirtualRectangle( e ) ) {
1857 if ( !isInOvRect() ) {
1858 setInOvRect( true );
1863 if ( isInOvRect() ) {
1864 setInOvRect( false );
1869 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
1878 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1879 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
1880 // cursor is over a tree node
1881 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
1882 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
1883 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
1884 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
1885 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
1886 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
1887 setCursor( CUT_CURSOR );
1890 setCursor( HAND_CURSOR );
1891 if ( getControlPanel().isNodeDescPopup() ) {
1892 showNodeDataPopup( e, node );
1897 setCursor( ARROW_CURSOR );
1902 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
1903 setCursor( ARROW_CURSOR );
1906 final public void mouseWheelMoved( final MouseWheelEvent e ) {
1907 final int notches = e.getWheelRotation();
1908 if ( inOvVirtualRectangle( e ) ) {
1909 if ( !isInOvRect() ) {
1910 setInOvRect( true );
1915 if ( isInOvRect() ) {
1916 setInOvRect( false );
1920 if ( e.isControlDown() ) {
1921 if ( notches < 0 ) {
1922 getTreeFontSet().increaseFontSize();
1923 getControlPanel().displayedPhylogenyMightHaveChanged( true );
1926 getTreeFontSet().decreaseFontSize();
1927 getControlPanel().displayedPhylogenyMightHaveChanged( true );
1930 else if ( e.isShiftDown() ) {
1931 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1932 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1933 if ( notches < 0 ) {
1934 for( int i = 0; i < ( -notches ); ++i ) {
1935 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
1936 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1940 for( int i = 0; i < notches; ++i ) {
1941 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
1942 if ( getStartingAngle() < 0 ) {
1943 setStartingAngle( TWO_PI + getStartingAngle() );
1945 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1950 if ( notches < 0 ) {
1951 for( int i = 0; i < ( -notches ); ++i ) {
1952 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1953 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1957 for( int i = 0; i < notches; ++i ) {
1958 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1959 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1965 if ( notches < 0 ) {
1966 for( int i = 0; i < ( -notches ); ++i ) {
1967 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1968 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
1969 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1970 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1974 for( int i = 0; i < notches; ++i ) {
1975 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1976 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1977 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1978 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1983 requestFocusInWindow();
1987 final void multiplyUrtFactor( final float f ) {
1991 final JApplet obtainApplet() {
1992 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1995 final private void openSeqWeb( final PhylogenyNode node ) {
1996 if ( !isCanOpenSeqWeb( node ) ) {
1997 cannotOpenBrowserWarningMessage( "sequence" );
2000 String uri_str = null;
2001 final Sequence seq = node.getNodeData().getSequence();
2002 final String source = seq.getAccession().getSource().toLowerCase();
2004 if ( source.toLowerCase().equals( "ncbi" ) ) {
2005 url = Constants.NCBI_ALL_DATABASE_SEARCH;
2008 final WebLink weblink = getConfiguration().getWebLink( source );
2009 url = weblink.getUrl().toString();
2012 uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
2014 catch ( final UnsupportedEncodingException e ) {
2015 Util.showErrorMessage( this, e.toString() );
2016 e.printStackTrace();
2018 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2020 JApplet applet = null;
2022 applet = obtainApplet();
2024 Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
2026 catch ( final IOException e ) {
2027 Util.showErrorMessage( this, e.toString() );
2028 e.printStackTrace();
2030 catch ( final URISyntaxException e ) {
2031 Util.showErrorMessage( this, e.toString() );
2032 e.printStackTrace();
2036 cannotOpenBrowserWarningMessage( "sequence" );
2040 final private void openTaxWeb( final PhylogenyNode node ) {
2041 if ( !isCanOpenTaxWeb( node ) ) {
2042 cannotOpenBrowserWarningMessage( "taxonomic" );
2045 String uri_str = null;
2046 final Taxonomy tax = node.getNodeData().getTaxonomy();
2047 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
2048 && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
2049 final String type = tax.getIdentifier().getProvider().toLowerCase();
2050 final WebLink weblink = getConfiguration().getWebLink( type );
2052 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
2054 catch ( final UnsupportedEncodingException e ) {
2055 Util.showErrorMessage( this, e.toString() );
2056 e.printStackTrace();
2059 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
2060 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
2062 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
2064 catch ( final URISyntaxException e ) {
2065 Util.showErrorMessage( this, e.toString() );
2067 e.printStackTrace();
2070 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
2072 uri_str = "http://www.eol.org/search?q="
2073 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
2075 catch ( final UnsupportedEncodingException e ) {
2076 Util.showErrorMessage( this, e.toString() );
2077 e.printStackTrace();
2080 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
2082 uri_str = "http://www.uniprot.org/taxonomy/?query="
2083 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
2085 catch ( final UnsupportedEncodingException e ) {
2086 Util.showErrorMessage( this, e.toString() );
2087 e.printStackTrace();
2090 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
2092 uri_str = "http://www.eol.org/search?q="
2093 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
2095 catch ( final UnsupportedEncodingException e ) {
2096 Util.showErrorMessage( this, e.toString() );
2097 e.printStackTrace();
2100 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2102 JApplet applet = null;
2104 applet = obtainApplet();
2106 Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
2108 catch ( final IOException e ) {
2109 Util.showErrorMessage( this, e.toString() );
2110 e.printStackTrace();
2112 catch ( final URISyntaxException e ) {
2113 Util.showErrorMessage( this, e.toString() );
2114 e.printStackTrace();
2118 cannotOpenBrowserWarningMessage( "taxonomic" );
2122 final void paintBranchCircular( final PhylogenyNode p,
2123 final PhylogenyNode c,
2125 final boolean radial_labels,
2126 final boolean to_pdf,
2127 final boolean to_graphics_file ) {
2128 final double angle = _urt_nodeid_angle_map.get( c.getId() );
2129 final double root_x = _root.getXcoord();
2130 final double root_y = _root.getYcoord();
2131 final double dx = root_x - p.getXcoord();
2132 final double dy = root_y - p.getYcoord();
2133 final double parent_radius = Math.sqrt( dx * dx + dy * dy );
2134 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
2135 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
2136 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
2137 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
2138 final double r2 = 2.0 * parent_radius;
2139 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
2141 drawLine( c.getXcoord(), c.getYcoord(), root_x + ( Math.cos( angle ) * parent_radius ), root_y
2142 + ( Math.sin( angle ) * parent_radius ), g );
2143 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c ) );
2144 if ( c.isExternal() ) {
2145 final boolean is_in_found_nodes = isInFoundNodes( c );
2146 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
2147 && ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor != 1 ) ) {
2150 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
2154 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
2155 final double angle = _urt_nodeid_angle_map.get( c.getId() );
2156 final double root_x = _root.getXSecondary();
2157 final double root_y = _root.getYSecondary();
2158 final double dx = root_x - p.getXSecondary();
2159 final double dy = root_y - p.getYSecondary();
2160 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
2161 final double parent_radius = Math.sqrt( dx * dx + dy * dy );
2162 g.setColor( getTreeColorSet().getOvColor() );
2163 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
2164 final double r2 = 2.0 * parent_radius;
2165 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
2167 drawLine( c.getXSecondary(), c.getYSecondary(), root_x + ( Math.cos( angle ) * parent_radius ), root_y
2168 + ( Math.sin( angle ) * parent_radius ), g );
2169 if ( isInFoundNodes( c ) ) {
2170 g.setColor( getTreeColorSet().getFoundColor() );
2171 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
2175 final private void paintBranchLength( final Graphics2D g,
2176 final PhylogenyNode node,
2177 final boolean to_pdf,
2178 final boolean to_graphics_file ) {
2179 g.setFont( getTreeFontSet().getSmallFont() );
2180 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2181 g.setColor( Color.BLACK );
2184 g.setColor( getTreeColorSet().getBranchLengthColor() );
2186 if ( !node.isRoot() ) {
2187 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2188 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2190 + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2192 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2193 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2195 + 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()
2281 && ( parent != null ) && parent.isHasAssignedEvent() ) )
2282 && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
2283 && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
2284 .isDuplication() ) ) {
2285 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
2286 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2287 if ( Math.abs( y2 - y1 ) <= TreePanel.HALF_BOX_SIZE ) {
2288 draw_vertical = false;
2292 y1 += TreePanel.HALF_BOX_SIZE;
2296 y1 -= TreePanel.HALF_BOX_SIZE + 1;
2299 y1 -= TreePanel.HALF_BOX_SIZE;
2304 if ( ( x2 - x1 ) <= TreePanel.HALF_BOX_SIZE ) {
2305 draw_horizontal = false;
2307 else if ( !draw_vertical ) {
2308 x1a += TreePanel.HALF_BOX_SIZE;
2310 if ( ( ( x2 - x1a ) > TreePanel.HALF_BOX_SIZE )
2311 && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
2312 .isDuplication() ) ) {
2313 x2a -= TreePanel.HALF_BOX_SIZE;
2316 if ( draw_vertical ) {
2317 if ( !to_graphics_file
2319 && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
2320 .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
2324 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2325 float x2c = x1 + EURO_D;
2329 drawLine( x1, y1, x2c, y2, g );
2331 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2333 y2_r = y2 - ROUNDED_D;
2337 drawLine( x1, y1, x1, y2_r, g );
2340 y2_r = y2 + ROUNDED_D;
2344 drawLine( x1, y1, x1, y2_r, g );
2348 drawLine( x1, y1, x1, y2, g );
2353 // draw the horizontal line
2354 if ( !to_graphics_file && !to_pdf
2355 && ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) {
2359 if ( draw_horizontal ) {
2360 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
2361 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2362 x1_r = x1a + ROUNDED_D;
2364 drawLine( x1_r, y2, x2a, y2, g );
2367 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2368 final float x1c = x1a + EURO_D;
2370 drawLine( x1c, y2, x2a, y2, g );
2374 drawLine( x1a, y2, x2a, y2, g );
2378 final double w = PhylogenyMethods.getBranchWidthValue( node );
2379 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2380 x1_r = x1a + ROUNDED_D;
2382 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
2385 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2386 final float x1c = x1a + EURO_D;
2388 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
2392 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
2396 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2401 final double diff = y2 - y2_r;
2402 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
2405 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
2410 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
2413 final void paintCircular( final Phylogeny phy,
2414 final double starting_angle,
2419 final boolean to_pdf,
2420 final boolean to_graphics_file ) {
2421 _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
2422 _root = phy.getRoot();
2423 _root.setXcoord( center_x );
2424 _root.setYcoord( center_y );
2425 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
2426 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
2427 double current_angle = starting_angle;
2429 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2430 final PhylogenyNode n = it.next();
2431 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
2432 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
2433 _urt_nodeid_angle_map.put( n.getId(), current_angle );
2434 _urt_nodeid_index_map.put( n.getId(), i++ );
2435 current_angle += ( TWO_PI / _circ_num_ext_nodes );
2437 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
2440 final void paintCircularLite( final Phylogeny phy,
2441 final double starting_angle,
2445 final Graphics2D g ) {
2446 _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
2447 _root = phy.getRoot();
2448 _root.setXSecondary( center_x );
2449 _root.setYSecondary( center_y );
2450 double current_angle = starting_angle;
2451 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2452 final PhylogenyNode n = it.next();
2453 n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) );
2454 n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) );
2455 _urt_nodeid_angle_map.put( n.getId(), current_angle );
2456 current_angle += ( TWO_PI / _circ_num_ext_nodes );
2458 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
2461 final private double paintCirculars( final PhylogenyNode n,
2462 final Phylogeny phy,
2463 final float center_x,
2464 final float center_y,
2465 final double radius,
2466 final boolean radial_labels,
2468 final boolean to_pdf,
2469 final boolean to_graphics_file ) {
2470 if ( n.isExternal() ) {
2471 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
2472 System.out.println( "no " + n + ", fucker!" );//TODO
2474 return _urt_nodeid_angle_map.get( n.getId() );
2477 final List<PhylogenyNode> descs = n.getDescendants();
2479 for( final PhylogenyNode desc : descs ) {
2480 sum += paintCirculars( desc,
2491 if ( !n.isRoot() ) {
2492 r = 1 - ( ( ( double ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
2494 final double theta = sum / descs.size();
2495 n.setXcoord( ( float ) ( center_x + r * radius * Math.cos( theta ) ) );
2496 n.setYcoord( ( float ) ( center_y + r * radius * Math.sin( theta ) ) );
2497 _urt_nodeid_angle_map.put( n.getId(), theta );
2498 for( final PhylogenyNode desc : descs ) {
2499 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
2505 final private void paintCircularsLite( final PhylogenyNode n,
2506 final Phylogeny phy,
2510 final Graphics2D g ) {
2511 if ( n.isExternal() ) {
2515 final List<PhylogenyNode> descs = n.getDescendants();
2516 for( final PhylogenyNode desc : descs ) {
2517 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
2520 if ( !n.isRoot() ) {
2521 r = 1 - ( ( ( float ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
2523 final double theta = _urt_nodeid_angle_map.get( n.getId() );
2524 n.setXSecondary( ( float ) ( center_x + radius * r * Math.cos( theta ) ) );
2525 n.setYSecondary( ( float ) ( center_y + radius * r * Math.sin( theta ) ) );
2526 for( final PhylogenyNode desc : descs ) {
2527 paintBranchCircularLite( n, desc, g );
2532 final private void paintCollapsedNode( final Graphics2D g,
2533 final PhylogenyNode node,
2534 final boolean to_graphics_file,
2535 final boolean to_pdf,
2536 final boolean is_in_found_nodes ) {
2537 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2538 g.setColor( Color.BLACK );
2540 else if ( is_in_found_nodes ) {
2541 g.setColor( getTreeColorSet().getFoundColor() );
2543 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
2544 g.setColor( getTaxonomyBasedColor( node ) );
2546 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
2547 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2548 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2551 g.setColor( getTreeColorSet().getCollapseFillColor() );
2553 double d = node.getAllExternalDescendants().size();
2555 d = ( 3 * _y_distance ) / 3;
2558 d = ( Math.log10( d ) * _y_distance ) / 2.5;
2560 if ( d < BOX_SIZE ) {
2564 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - TreePanel.BOX_SIZE ), ForesterUtil
2565 .roundToInt( node.getYcoord() ) );
2566 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), ForesterUtil
2567 .roundToInt( node.getYcoord() - d ) );
2568 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), ForesterUtil
2569 .roundToInt( node.getYcoord() + d ) );
2570 g.fillPolygon( _polygon );
2571 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
2575 final public void paintComponent( final Graphics g ) {
2576 // Dimension currentSize = getSize();
2577 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
2578 // call the 'java.awt.Component.createImage(...)' method to get an
2580 // offscreenImage = createImage( currentSize.width, currentSize.height );
2581 // offscreenGraphics = offscreenImage.getGraphics();
2582 // offscreenDimension = currentSize;
2584 // super.paintComponent( g ); //why?
2585 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
2586 final Graphics2D g2d = ( Graphics2D ) g;
2587 g2d.setRenderingHints( _rendering_hints );
2588 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
2589 //g.drawImage( offscreenImage, 0, 0, this );
2593 public void update( final Graphics g ) {
2597 final private void paintConfidenceValues( final Graphics2D g,
2598 final PhylogenyNode node,
2599 final boolean to_pdf,
2600 final boolean to_graphics_file ) {
2601 String conf_str = "";
2602 final List<Confidence> confidences = node.getBranchData().getConfidences();
2603 if ( confidences.size() == 1 ) {
2604 final double value = node.getBranchData().getConfidence( 0 ).getValue();
2605 if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
2608 conf_str = FORMATTER_CONFIDENCE.format( value );
2610 else if ( confidences.size() > 1 ) {
2611 boolean one_ok = false;
2612 boolean not_first = false;
2613 Collections.sort( confidences );
2614 final StringBuilder sb = new StringBuilder();
2615 for( final Confidence confidence : confidences ) {
2616 final double value = confidence.getValue();
2617 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
2618 if ( value >= getOptions().getMinConfidenceValue() ) {
2627 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
2628 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
2632 conf_str = sb.toString();
2635 if ( conf_str.length() > 0 ) {
2636 final double parent_x = node.getParent().getXcoord();
2637 double x = node.getXcoord();
2638 g.setFont( getTreeFontSet().getSmallFont() );
2639 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2642 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2645 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2646 g.setColor( Color.BLACK );
2649 g.setColor( getTreeColorSet().getConfidenceColor() );
2652 .drawString( conf_str, parent_x
2653 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ), ( node
2654 .getYcoord() + getTreeFontSet()._small_max_ascent ) - 1, g );
2658 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
2659 g.setColor( getTreeColorSet().getFoundColor() );
2660 g.fillRect( x - TreePanel.HALF_BOX_SIZE, y - TreePanel.HALF_BOX_SIZE, TreePanel.BOX_SIZE, TreePanel.BOX_SIZE );
2663 final private void paintGainedAndLostCharacters( final Graphics2D g,
2664 final PhylogenyNode node,
2665 final String gained,
2666 final String lost ) {
2667 if ( node.getParent() != null ) {
2668 final double parent_x = node.getParent().getXcoord();
2669 final double x = node.getXcoord();
2670 g.setFont( getTreeFontSet().getLargeFont() );
2671 g.setColor( getTreeColorSet().getGainedCharactersColor() );
2672 if ( Constants.SPECIAL_CUSTOM ) {
2673 g.setColor( Color.BLUE );
2676 .drawString( gained, parent_x
2677 + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ), ( node
2678 .getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ), g );
2679 g.setColor( getTreeColorSet().getLostCharactersColor() );
2680 TreePanel.drawString( lost,
2681 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
2682 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
2688 * Draw a box at the indicated node.
2695 final private void paintNodeBox( final double x,
2697 final PhylogenyNode node,
2699 final boolean to_pdf,
2700 final boolean to_graphics_file,
2701 final boolean is_in_found_nodes ) {
2702 if ( node.isCollapse() ) {
2705 // if this node should be highlighted, do so
2706 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
2707 g.setColor( getTreeColorSet().getFoundColor() );
2708 drawOval( x - 8, y - 8, 16, 16, g );
2709 drawOval( x - 9, y - 8, 17, 17, g );
2710 drawOval( x - 9, y - 9, 18, 18, g );
2712 if ( is_in_found_nodes ) {
2713 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
2716 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2717 g.setColor( Color.BLACK );
2719 else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) {
2720 final Event event = node.getNodeData().getEvent();
2721 if ( event.isDuplication() ) {
2722 g.setColor( getTreeColorSet().getDuplicationBoxColor() );
2724 else if ( event.isSpeciation() ) {
2725 g.setColor( getTreeColorSet().getSpecBoxColor() );
2727 else if ( event.isSpeciationOrDuplication() ) {
2728 g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() );
2732 assignGraphicsForNodeBoxWithColorForParentBranch( node, g );
2734 if ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file )
2735 || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
2736 if ( to_pdf || to_graphics_file ) {
2737 if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
2738 drawOvalFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
2742 drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
2748 final private void paintNodeData( final Graphics2D g,
2749 final PhylogenyNode node,
2750 final boolean to_graphics_file,
2751 final boolean to_pdf,
2752 final boolean is_in_found_nodes ) {
2753 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
2756 if ( getOptions().isShowBranchLengthValues()
2757 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
2758 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
2759 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) ) {
2760 paintBranchLength( g, node, to_pdf, to_graphics_file );
2762 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
2766 if ( getControlPanel().isShowTaxonomyImages()
2767 && ( getImageMap() != null )
2768 && !getImageMap().isEmpty()
2769 && node.getNodeData().isHasTaxonomy()
2770 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
2771 .getUris().isEmpty() ) ) {
2772 x += drawTaxonomyImage( node.getXcoord() + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord(), node, g );
2774 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
2775 .isShowTaxonomyCommonNames() )
2776 && node.getNodeData().isHasTaxonomy() ) {
2777 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
2779 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2780 g.setColor( Color.BLACK );
2782 else if ( is_in_found_nodes ) {
2783 g.setColor( getTreeColorSet().getFoundColor() );
2785 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
2786 g.setColor( getTaxonomyBasedColor( node ) );
2788 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
2789 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2790 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
2792 else if ( to_pdf ) {
2793 g.setColor( Color.BLACK );
2796 g.setColor( getTreeColorSet().getSequenceColor() );
2799 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
2801 _sb.append( node.getAllExternalDescendants().size() );
2804 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
2805 if ( _sb.length() > 0 ) {
2808 _sb.append( node.getName() );
2810 if ( node.getNodeData().isHasSequence() ) {
2811 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
2812 if ( _sb.length() > 0 ) {
2815 _sb.append( node.getNodeData().getSequence().getSymbol() );
2817 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
2818 if ( _sb.length() > 0 ) {
2821 _sb.append( node.getNodeData().getSequence().getName() );
2823 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
2824 if ( _sb.length() > 0 ) {
2827 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
2828 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
2831 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
2834 g.setFont( getTreeFontSet().getLargeFont() );
2835 if ( is_in_found_nodes ) {
2836 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
2838 double down_shift_factor = 3.0;
2839 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
2840 down_shift_factor = 1;
2842 // GUILHEM_BEG ______________
2843 final double posX = node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE;
2844 final double posY = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
2845 final int CONFIDENCE_LEFT_MARGIN = 4;
2846 final String sNodeText = _sb.toString();
2847 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
2848 && ( _query_sequence != null ) ) {
2849 int nodeTextBoundsWidth = 0;
2850 if ( sNodeText.length() > 0 ) {
2851 final Rectangle2D node_text_bounds = new TextLayout( sNodeText, 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 ) posX - 1, ( int ) posY - 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 = posX;
2874 if ( sNodeText.length() > 0 ) {
2875 confidenceX += new TextLayout( sNodeText, 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, posY, 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 ) posY, ( int ) linePosX + x
2894 + nodeTextBoundsWidth, 3 + ( int ) posY );
2901 if ( sNodeText.length() > 0 ) {
2902 TreePanel.drawString( sNodeText, posX, posY, 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(), node
2972 + x + 4 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
2973 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
2975 paintGainedAndLostCharacters( g, node, "+"
2976 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
2977 + node.getNodeData().getBinaryCharacters().getLostCount() );
2983 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
2984 final List<Uri> us = new ArrayList<Uri>();
2985 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
2986 for( final Uri uri : t.getUris() ) {
2991 for( final Uri uri : us ) {
2992 if ( uri != null ) {
2993 final String uri_str = uri.getValue().toString().toLowerCase();
2994 if ( getImageMap().containsKey( uri_str ) ) {
2995 final BufferedImage bi = getImageMap().get( uri_str );
2996 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
2997 double scaling_factor = 1;
2998 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
2999 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
3000 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
3002 // y = y - ( 0.9 * getYdistance() );
3003 final double hs = bi.getHeight() * scaling_factor;
3004 double ws = bi.getWidth() * scaling_factor + offset;
3005 final double my_y = y - ( 0.5 * hs );
3006 final int x_w = ( int ) ( x + ws + 0.5 );
3007 final int y_h = ( int ) ( my_y + hs + 0.5 );
3008 if ( ( x_w - x > 7 ) && ( y_h - my_y > 7 ) ) {
3009 g.drawImage( bi, ( int ) ( x + 0.5 + offset ), ( int ) ( my_y + 0.5 ), x_w, y_h, 0, 0, bi
3010 .getWidth(), bi.getHeight(), null );
3024 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
3025 final PhylogenyNode node,
3026 final boolean to_pdf,
3027 final boolean to_graphics_file,
3028 final boolean radial_labels,
3029 final double ur_angle,
3030 final boolean is_in_found_nodes ) {
3031 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
3034 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3035 g.setColor( Color.BLACK );
3037 else if ( is_in_found_nodes ) {
3038 g.setColor( getTreeColorSet().getFoundColor() );
3040 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3041 g.setColor( getTaxonomyBasedColor( node ) );
3044 g.setColor( getTreeColorSet().getSequenceColor() );
3048 if ( node.getNodeData().isHasTaxonomy()
3049 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3050 .isShowTaxonomyCommonNames() ) ) {
3051 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3052 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
3053 _sb.append( taxonomy.getTaxonomyCode() );
3056 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
3057 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
3058 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3059 _sb.append( taxonomy.getScientificName() );
3061 _sb.append( taxonomy.getCommonName() );
3064 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3065 _sb.append( taxonomy.getScientificName() );
3068 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3069 _sb.append( taxonomy.getCommonName() );
3073 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
3074 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3075 _sb.append( taxonomy.getScientificName() );
3079 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
3080 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3081 _sb.append( taxonomy.getCommonName() );
3086 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3088 _sb.append( node.getAllExternalDescendants().size() );
3091 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3092 if ( _sb.length() > 0 ) {
3095 _sb.append( node.getName() );
3097 if ( node.getNodeData().isHasSequence() ) {
3098 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3099 if ( _sb.length() > 0 ) {
3102 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3103 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3106 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3108 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3109 if ( _sb.length() > 0 ) {
3112 _sb.append( node.getNodeData().getSequence().getName() );
3115 g.setFont( getTreeFontSet().getLargeFont() );
3116 if ( is_in_found_nodes ) {
3117 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3119 if ( _sb.length() > 1 ) {
3120 final String sb_str = _sb.toString();
3122 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3123 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
3126 m = ( float ) ( ur_angle % TWO_PI );
3128 _at = g.getTransform();
3129 boolean need_to_reset = false;
3130 final float x_coord = node.getXcoord();
3131 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
3132 if ( radial_labels ) {
3133 need_to_reset = true;
3134 boolean left = false;
3135 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3139 g.rotate( m, x_coord, node.getYcoord() );
3141 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
3145 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3146 need_to_reset = true;
3147 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
3150 TreePanel.drawString( sb_str, x_coord, y_coord, g );
3151 if ( need_to_reset ) {
3152 g.setTransform( _at );
3157 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
3158 if ( node.isCollapse() ) {
3159 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
3160 paintCollapsedNode( g, node, false, false, false );
3164 if ( isInFoundNodes( node ) ) {
3165 g.setColor( getTreeColorSet().getFoundColor() );
3166 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
3169 if ( !node.isExternal() && !node.isCollapse() ) {
3170 boolean first_child = true;
3172 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3173 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3174 final PhylogenyNode child_node = node.getChildNode( i );
3176 if ( !isUniformBranchLengthsForCladogram() ) {
3177 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3180 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
3182 if ( first_child ) {
3183 first_child = false;
3184 y2 = node.getYSecondary()
3185 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
3186 .getNumberOfExternalNodes() ) );
3189 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3191 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
3192 new_x = x2 + node.getXSecondary();
3193 final float diff_y = node.getYSecondary() - y2;
3194 final float diff_x = node.getXSecondary() - new_x;
3195 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
3196 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
3198 child_node.setXSecondary( new_x );
3199 child_node.setYSecondary( y2 );
3200 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3205 final private void paintNodeRectangular( final Graphics2D g,
3206 final PhylogenyNode node,
3207 final boolean to_pdf,
3208 final boolean dynamically_hide,
3209 final int dynamic_hiding_factor,
3210 final boolean to_graphics_file ) {
3211 final boolean is_in_found_nodes = isInFoundNodes( node );
3212 if ( node.isCollapse() ) {
3213 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
3214 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3218 if ( node.isExternal() ) {
3219 ++_external_node_index;
3221 // Confidence values
3222 if ( getControlPanel().isShowBootstrapValues()
3223 && !node.isExternal()
3225 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
3226 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3227 && node.getBranchData().isHasConfidences() ) {
3228 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
3230 // Draw a line to root:
3231 if ( node.isRoot() && _phylogeny.isRooted() ) {
3232 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
3235 float new_x_min = Float.MAX_VALUE;
3236 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
3237 float min_dist = 1.5f;
3238 if ( !disallow_shortcutting ) {
3239 // System.out.println( dynamic_hiding_factor );
3240 if ( dynamic_hiding_factor > 4000 ) {
3243 else if ( dynamic_hiding_factor > 1000 ) {
3246 else if ( dynamic_hiding_factor > 100 ) {
3250 if ( !node.isExternal() && !node.isCollapse() ) {
3251 boolean first_child = true;
3253 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3254 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3255 final PhylogenyNode child_node = node.getChildNode( i );
3257 if ( !isUniformBranchLengthsForCladogram() ) {
3258 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3261 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
3263 if ( first_child ) {
3264 first_child = false;
3265 y2 = node.getYcoord()
3266 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
3269 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3271 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
3272 new_x = x2 + node.getXcoord();
3273 if ( dynamically_hide && ( x2 < new_x_min ) ) {
3276 final float diff_y = node.getYcoord() - y2;
3277 final float diff_x = node.getXcoord() - new_x;
3278 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
3279 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
3280 paintBranchRectangular( g,
3289 child_node.setXcoord( new_x );
3290 child_node.setYcoord( y2 );
3291 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3294 if ( dynamically_hide
3295 && !is_in_found_nodes
3296 && ( ( node.isExternal() && ( _external_node_index % dynamic_hiding_factor != 1 ) ) || ( !node
3297 .isExternal() && ( ( new_x_min < 20 ) || ( _y_distance * node.getNumberOfExternalNodes() < getTreeFontSet()._fm_large
3298 .getHeight() ) ) ) ) ) {
3301 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3302 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
3305 final private void paintNodeWithRenderableData( final Graphics2D g,
3306 final PhylogenyNode node,
3307 final boolean to_graphics_file,
3308 final boolean to_pdf ) {
3309 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
3312 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
3315 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
3316 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
3317 RenderableDomainArchitecture rds = null;
3318 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
3320 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
3322 catch ( final ClassCastException cce ) {
3323 cce.printStackTrace();
3326 rds.setRenderingHeight( 6 );
3328 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) {
3329 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
3331 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3332 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
3334 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
3338 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
3339 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
3340 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
3341 getStatisticsForExpressionValues(),
3342 getConfiguration() );
3344 PhylogenyNode my_node = node;
3345 if ( !getControlPanel().isDrawPhylogram() ) {
3346 my_node = getPhylogeny().getFirstExternalNode();
3348 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
3349 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
3351 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
3352 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
3354 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
3359 final private void paintOvRectangle( final Graphics2D g ) {
3360 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
3361 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
3362 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
3363 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
3364 final float width = getOvMaxWidth() / w_ratio;
3365 final float height = getOvMaxHeight() / h_ratio;
3366 final float x = getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / x_ratio;
3367 final float y = getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / y_ratio;
3368 g.setColor( getTreeColorSet().getFoundColor() );
3369 getOvRectangle().setRect( x, y, width, height );
3370 if ( ( width < 6 ) && ( height < 6 ) ) {
3371 drawRectFilled( x, y, 6, 6, g );
3372 getOvVirtualRectangle().setRect( x, y, 6, 6 );
3374 else if ( width < 6 ) {
3375 drawRectFilled( x, y, 6, height, g );
3376 getOvVirtualRectangle().setRect( x, y, 6, height );
3378 else if ( height < 6 ) {
3379 drawRectFilled( x, y, width, 6, g );
3380 getOvVirtualRectangle().setRect( x, y, width, 6 );
3383 drawRect( x, y, width, height, g );
3384 if ( isInOvRect() ) {
3385 drawRect( x + 1, y + 1, width - 2, height - 2, g );
3387 getOvVirtualRectangle().setRect( x, y, width, height );
3391 final void paintPhylogeny( final Graphics2D g,
3392 final boolean to_pdf,
3393 final boolean to_graphics_file,
3394 final int graphics_file_width,
3395 final int graphics_file_height,
3396 final int graphics_file_x,
3397 final int graphics_file_y ) {
3399 // System.out.println( "p" + ( xxx++ ) );
3400 _query_sequence = _control_panel.getSelectedQuerySequence();
3402 // Color the background
3404 final Rectangle r = getVisibleRect();
3405 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
3406 g.setColor( getTreeColorSet().getBackgroundColor() );
3407 if ( !to_graphics_file ) {
3411 if ( getOptions().isPrintBlackAndWhite() ) {
3412 g.setColor( Color.WHITE );
3414 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
3418 if ( !to_graphics_file ) {
3419 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
3420 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
3424 g.setPaint( new GradientPaint( graphics_file_x,
3426 getTreeColorSet().getBackgroundColor(),
3428 graphics_file_y + graphics_file_height,
3429 getTreeColorSet().getBackgroundColorGradientBottom() ) );
3430 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
3433 g.setStroke( new BasicStroke( 1 ) );
3436 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
3438 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3439 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3440 _external_node_index = 0;
3441 // Position starting X of tree
3442 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
3443 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
3445 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
3446 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
3447 .getDistanceToParent() * getXcorrectionFactor() ) ) );
3450 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
3452 // Position starting Y of tree
3453 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
3454 + ( TreePanel.MOVE / 2.0f ) );
3455 final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
3456 if ( getControlPanel().isDynamicallyHideData() ) {
3457 if ( dynamic_hiding_factor > 1 ) {
3458 getControlPanel().setDynamicHidingIsOn( true );
3461 getControlPanel().setDynamicHidingIsOn( false );
3464 final PhylogenyNodeIterator it;
3465 for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3466 paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
3467 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
3469 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
3470 if ( !( to_graphics_file || to_pdf ) ) {
3473 getVisibleRect().y + getVisibleRect().height,
3478 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
3481 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3482 paintPhylogenyLite( g );
3485 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
3486 if ( getControlPanel().getDynamicallyHideData() != null ) {
3487 getControlPanel().setDynamicHidingIsOn( false );
3489 final double angle = getStartingAngle();
3490 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
3491 _dynamic_hiding_factor = 0;
3492 if ( getControlPanel().isDynamicallyHideData() ) {
3493 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
3494 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
3496 if ( getControlPanel().getDynamicallyHideData() != null ) {
3497 if ( _dynamic_hiding_factor > 1 ) {
3498 getControlPanel().setDynamicHidingIsOn( true );
3501 getControlPanel().setDynamicHidingIsOn( false );
3504 paintUnrooted( _phylogeny.getRoot(),
3506 ( float ) ( angle + 2 * Math.PI ),
3511 if ( getOptions().isShowScale() ) {
3512 if ( !( to_graphics_file || to_pdf ) ) {
3515 getVisibleRect().y + getVisibleRect().height,
3520 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
3523 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3524 g.setColor( getTreeColorSet().getOvColor() );
3525 paintUnrootedLite( _phylogeny.getRoot(),
3527 angle + 2 * Math.PI,
3529 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
3530 paintOvRectangle( g );
3533 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3534 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
3535 final int d = radius + MOVE + getLongestExtNodeInfo();
3536 _dynamic_hiding_factor = 0;
3537 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
3538 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
3539 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
3541 if ( getControlPanel().getDynamicallyHideData() != null ) {
3542 if ( _dynamic_hiding_factor > 1 ) {
3543 getControlPanel().setDynamicHidingIsOn( true );
3546 getControlPanel().setDynamicHidingIsOn( false );
3549 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
3550 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3551 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
3552 : getOvMaxWidth() / 2 );
3553 double x_scale = 1.0;
3554 double y_scale = 1.0;
3555 int x_pos = getVisibleRect().x + getOvXPosition();
3556 int y_pos = getVisibleRect().y + getOvYPosition();
3557 if ( getWidth() > getHeight() ) {
3558 x_scale = ( double ) getHeight() / getWidth();
3559 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
3562 y_scale = ( double ) getWidth() / getHeight();
3563 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
3565 _at = g.getTransform();
3566 g.scale( x_scale, y_scale );
3567 paintCircularLite( _phylogeny,
3571 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
3574 g.setTransform( _at );
3575 paintOvRectangle( g );
3580 final private void paintPhylogenyLite( final Graphics2D g ) {
3581 //System.out.println( getVisibleRect().x + " " + getVisibleRect().y );
3584 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
3585 .getWidth() ) ) ) );
3586 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
3587 final PhylogenyNodeIterator it;
3588 for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3589 paintNodeLite( g, it.next() );
3591 paintOvRectangle( g );
3595 * Paint the root branch. (Differs from others because it will always be a
3596 * single horizontal line).
3597 * @param to_graphics_file
3599 * @return new x1 value
3601 final private void paintRootBranch( final Graphics2D g,
3604 final PhylogenyNode root,
3605 final boolean to_pdf,
3606 final boolean to_graphics_file ) {
3607 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
3608 float d = getXdistance();
3609 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
3610 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
3612 if ( d < MIN_ROOT_LENGTH ) {
3613 d = MIN_ROOT_LENGTH;
3615 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
3616 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
3619 final double w = PhylogenyMethods.getBranchWidthValue( root );
3620 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
3622 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
3625 final private void paintScale( final Graphics2D g,
3628 final boolean to_pdf,
3629 final boolean to_graphics_file ) {
3631 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
3633 final int y2 = y1 - 8;
3634 final int y3 = y1 - 4;
3635 g.setFont( getTreeFontSet().getSmallFont() );
3636 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3637 g.setColor( Color.BLACK );
3640 g.setColor( getTreeColorSet().getBranchLengthColor() );
3642 drawLine( x1, y1, x1, y2, g );
3643 drawLine( x2, y1, x2, y2, g );
3644 drawLine( x1, y3, x2, y3, g );
3645 if ( getScaleLabel() != null ) {
3646 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
3650 final private int paintTaxonomy( final Graphics2D g,
3651 final PhylogenyNode node,
3652 final boolean is_in_found_nodes,
3653 final boolean to_pdf,
3654 final boolean to_graphics_file,
3655 final double x_shift ) {
3656 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3657 g.setFont( getTreeFontSet().getLargeItalicFont() );
3658 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3659 g.setColor( Color.BLACK );
3661 else if ( is_in_found_nodes ) {
3662 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
3663 g.setColor( getTreeColorSet().getFoundColor() );
3665 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3666 g.setColor( getTaxonomyBasedColor( node ) );
3668 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3669 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3670 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3672 else if ( to_pdf ) {
3673 g.setColor( Color.BLACK );
3676 g.setColor( getTreeColorSet().getTaxonomyColor() );
3678 final double start_x = node.getXcoord() + 3 + TreePanel.HALF_BOX_SIZE + x_shift;
3679 final double start_y = node.getYcoord()
3680 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
3682 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
3683 _sb.append( taxonomy.getTaxonomyCode() );
3686 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
3687 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
3688 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3689 if ( getOptions().isAbbreviateScientificTaxonNames()
3690 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
3691 abbreviateScientificName( taxonomy.getScientificName() );
3694 _sb.append( taxonomy.getScientificName() );
3697 _sb.append( taxonomy.getCommonName() );
3700 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3701 if ( getOptions().isAbbreviateScientificTaxonNames()
3702 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
3703 abbreviateScientificName( taxonomy.getScientificName() );
3706 _sb.append( taxonomy.getScientificName() );
3710 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3711 _sb.append( taxonomy.getCommonName() );
3715 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
3716 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3717 if ( getOptions().isAbbreviateScientificTaxonNames()
3718 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
3719 abbreviateScientificName( taxonomy.getScientificName() );
3722 _sb.append( taxonomy.getScientificName() );
3727 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
3728 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3729 _sb.append( taxonomy.getCommonName() );
3733 final String label = _sb.toString();
3735 if ( ( label.length() > 0 ) && ( node.getNodeData().isHasSequence() )
3736 && node.getNodeData().getSequence().equals( _query_sequence ) ) {
3737 // invert font color and background color to show that this is the query sequence
3738 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
3742 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
3743 g.setColor( getTreeColorSet().getBackgroundColor() );
3746 TreePanel.drawString( label, start_x, start_y, g );
3747 if ( is_in_found_nodes ) {
3748 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
3751 return getTreeFontSet()._fm_large_italic.stringWidth( label );
3755 private void abbreviateScientificName( final String sn ) {
3756 final String[] a = sn.split( "\\s+" );
3757 _sb.append( a[ 0 ].substring( 0, 1 ) );
3758 _sb.append( a[ 1 ].substring( 0, 2 ) );
3759 if ( a.length > 2 ) {
3760 for( int i = 2; i < a.length; i++ ) {
3762 _sb.append( a[ i ] );
3767 final private void paintUnrooted( final PhylogenyNode n,
3768 final double low_angle,
3769 final double high_angle,
3770 final boolean radial_labels,
3772 final boolean to_pdf,
3773 final boolean to_graphics_file ) {
3775 n.setXcoord( getWidth() / 2 );
3776 n.setYcoord( getHeight() / 2 );
3777 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
3779 if ( n.isExternal() ) {
3780 paintNodeDataUnrootedCirc( g,
3785 ( high_angle + low_angle ) / 2,
3786 isInFoundNodes( n ) );
3789 final float num_enclosed = n.getNumberOfExternalNodes();
3790 final float x = n.getXcoord();
3791 final float y = n.getYcoord();
3792 double current_angle = low_angle;
3793 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
3794 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
3795 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
3796 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
3797 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
3798 final PhylogenyNode desc = n.getChildNode( i );
3799 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
3800 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
3801 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
3802 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
3805 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
3808 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
3811 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
3812 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
3814 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
3815 if ( desc.getDistanceToParent() < 0 ) {
3819 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
3823 length = getUrtFactor();
3825 final double mid_angle = current_angle + arc_size / 2;
3826 final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
3827 final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
3828 desc.setXcoord( new_x );
3829 desc.setYcoord( new_y );
3830 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
3831 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
3832 current_angle += arc_size;
3833 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
3834 drawLine( x, y, new_x, new_y, g );
3838 final private void paintUnrootedLite( final PhylogenyNode n,
3839 final double low_angle,
3840 final double high_angle,
3842 final float urt_ov_factor ) {
3844 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / 2 );
3845 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / 2 );
3846 n.setXSecondary( x_pos );
3847 n.setYSecondary( y_pos );
3849 if ( n.isExternal() ) {
3852 final float num_enclosed = n.getNumberOfExternalNodes();
3853 final float x = n.getXSecondary();
3854 final float y = n.getYSecondary();
3855 double current_angle = low_angle;
3856 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
3857 final PhylogenyNode desc = n.getChildNode( i );
3858 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
3859 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
3861 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
3862 if ( desc.getDistanceToParent() < 0 ) {
3866 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
3870 length = urt_ov_factor;
3872 final double mid_angle = current_angle + arc_size / 2;
3873 final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
3874 final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
3875 desc.setXSecondary( new_x );
3876 desc.setYSecondary( new_y );
3877 if ( isInFoundNodes( desc ) ) {
3878 g.setColor( getTreeColorSet().getFoundColor() );
3879 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
3880 g.setColor( getTreeColorSet().getOvColor() );
3882 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
3883 current_angle += arc_size;
3884 drawLine( x, y, new_x, new_y, g );
3888 final private void pasteSubtree( final PhylogenyNode node ) {
3889 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
3890 errorMessageNoCutCopyPasteInUnrootedDisplay();
3893 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
3894 JOptionPane.showMessageDialog( this,
3895 "No tree in buffer (need to copy or cut a subtree first)",
3896 "Attempt to paste with empty buffer",
3897 JOptionPane.ERROR_MESSAGE );
3900 final String label = getASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
3901 final Object[] options = { "As sibling", "As descendant", "Cancel" };
3902 final int r = JOptionPane.showOptionDialog( this,
3903 "How to paste subtree" + label + "?",
3905 JOptionPane.CLOSED_OPTION,
3906 JOptionPane.QUESTION_MESSAGE,
3910 boolean paste_as_sibling = true;
3912 paste_as_sibling = false;
3914 else if ( r != 0 ) {
3917 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
3918 buffer_phy.setAllNodesToNotCollapse();
3919 buffer_phy.preOrderReId();
3920 buffer_phy.setRooted( true );
3921 boolean need_to_show_whole = false;
3922 if ( paste_as_sibling ) {
3923 if ( node.isRoot() ) {
3924 JOptionPane.showMessageDialog( this,
3925 "Cannot paste sibling to root",
3926 "Attempt to paste sibling to root",
3927 JOptionPane.ERROR_MESSAGE );
3930 buffer_phy.addAsSibling( node );
3933 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
3934 need_to_show_whole = true;
3935 _phylogeny = buffer_phy;
3938 buffer_phy.addAsChild( node );
3941 if ( getCopiedAndPastedNodes() == null ) {
3942 setCopiedAndPastedNodes( new HashSet<Integer>() );
3944 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
3945 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
3946 for( final PhylogenyNode n : nodes ) {
3947 node_ids.add( n.getId() );
3949 node_ids.add( node.getId() );
3950 getCopiedAndPastedNodes().addAll( node_ids );
3951 _phylogeny.externalNodesHaveChanged();
3952 _phylogeny.hashIDs();
3953 _phylogeny.recalculateNumberOfExternalDescendants( true );
3954 resetNodeIdToDistToLeafMap();
3956 if ( need_to_show_whole ) {
3957 getControlPanel().showWhole();
3962 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
3963 throws PrinterException {
3964 if ( page_index > 0 ) {
3965 return ( NO_SUCH_PAGE );
3968 final Graphics2D g2d = ( Graphics2D ) g;
3969 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
3970 // Turn off double buffering !?
3971 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
3972 // Turn double buffering back on !?
3973 return ( PAGE_EXISTS );
3977 final void recalculateMaxDistanceToRoot() {
3978 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
3982 * Remove all edit-node frames
3984 final void removeAllEditNodeJFrames() {
3985 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
3986 if ( _node_frames[ i ] != null ) {
3987 _node_frames[ i ].dispose();
3988 _node_frames[ i ] = null;
3991 _node_frame_index = 0;
3995 * Remove a node-edit frame.
3997 final void removeEditNodeFrame( final int i ) {
3998 _node_frame_index--;
3999 _node_frames[ i ] = null;
4000 if ( i < _node_frame_index ) {
4001 for( int j = 0; j < _node_frame_index - 1; j++ ) {
4002 _node_frames[ j ] = _node_frames[ j + 1 ];
4004 _node_frames[ _node_frame_index ] = null;
4008 final void reRoot( final PhylogenyNode node ) {
4009 if ( !getPhylogeny().isRerootable() ) {
4010 JOptionPane.showMessageDialog( this,
4011 "This is not rerootable",
4013 JOptionPane.WARNING_MESSAGE );
4016 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4017 JOptionPane.showMessageDialog( this,
4018 "Cannot reroot in unrooted display type",
4019 "Attempt to reroot tree in unrooted display",
4020 JOptionPane.WARNING_MESSAGE );
4023 getPhylogeny().reRoot( node );
4024 getPhylogeny().recalculateNumberOfExternalDescendants( true );
4025 resetNodeIdToDistToLeafMap();
4026 resetPreferredSize();
4027 getMainPanel().adjustJScrollPane();
4029 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4030 getControlPanel().showWhole();
4034 final void resetNodeIdToDistToLeafMap() {
4035 _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
4038 final void resetPreferredSize() {
4039 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
4045 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
4046 if ( getControlPanel().isDrawPhylogram() ) {
4048 + getLongestExtNodeInfo()
4050 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
4053 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4055 + getLongestExtNodeInfo()
4056 + ForesterUtil.roundToInt( getXdistance()
4057 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
4061 + getLongestExtNodeInfo()
4062 + ForesterUtil.roundToInt( getXdistance()
4063 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
4066 setPreferredSize( new Dimension( x, y ) );
4069 final void setArrowCursor() {
4070 setCursor( ARROW_CURSOR );
4074 final void setControlPanel( final ControlPanel atv_control ) {
4075 _control_panel = atv_control;
4078 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4079 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4082 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4083 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4086 final void setEdited( final boolean edited ) {
4090 final void setFoundNodes( final Set<Integer> found_nodes ) {
4091 _found_nodes = found_nodes;
4094 final private void setInOv( final boolean in_ov ) {
4098 final void setInOvRect( final boolean in_ov_rect ) {
4099 _in_ov_rect = in_ov_rect;
4102 final void setLargeFonts() {
4103 getTreeFontSet().largeFonts();
4106 final void setLastMouseDragPointX( final float x ) {
4107 _last_drag_point_x = x;
4110 final void setLastMouseDragPointY( final float y ) {
4111 _last_drag_point_y = y;
4114 final void setLongestExtNodeInfo( final int i ) {
4115 _longest_ext_node_info = i;
4118 final void setMediumFonts() {
4119 getTreeFontSet().mediumFonts();
4122 final private void setOvMaxHeight( final float ov_max_height ) {
4123 _ov_max_height = ov_max_height;
4126 final private void setOvMaxWidth( final float ov_max_width ) {
4127 _ov_max_width = ov_max_width;
4130 final void setOvOn( final boolean ov_on ) {
4134 final private void setOvXcorrectionFactor( final float f ) {
4135 _ov_x_correction_factor = f;
4138 final private void setOvXDistance( final float ov_x_distance ) {
4139 _ov_x_distance = ov_x_distance;
4142 final private void setOvXPosition( final int ov_x_position ) {
4143 _ov_x_position = ov_x_position;
4146 final private void setOvYDistance( final float ov_y_distance ) {
4147 _ov_y_distance = ov_y_distance;
4150 final private void setOvYPosition( final int ov_y_position ) {
4151 _ov_y_position = ov_y_position;
4154 final private void setOvYStart( final int ov_y_start ) {
4155 _ov_y_start = ov_y_start;
4159 * Set parameters for printing the displayed tree
4164 final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
4165 // updateStyle(); not needed?
4166 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4168 if ( recalc_longest_ext_node_info ) {
4169 calculateLongestExtNodeInfo();
4171 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
4172 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
4173 if ( ext_nodes == 1 ) {
4174 ext_nodes = max_depth;
4175 if ( ext_nodes < 1 ) {
4182 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4183 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
4184 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
4187 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
4188 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
4190 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
4191 if ( xdist < 0.0 ) {
4194 if ( ov_xdist < 0.0 ) {
4197 if ( ydist < 0.0 ) {
4200 setXdistance( xdist );
4201 setYdistance( ydist );
4202 setOvXDistance( ov_xdist );
4203 final double height = _phylogeny.getHeight();
4205 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
4206 setXcorrectionFactor( corr > 0 ? corr : 0 );
4207 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
4208 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
4211 setXcorrectionFactor( 0 );
4212 setOvXcorrectionFactor( 0 );
4214 _circ_max_depth = max_depth;
4219 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
4220 _graphics_type = graphics_type;
4224 final private void setScaleDistance( final double scale_distance ) {
4225 _scale_distance = scale_distance;
4228 final private void setScaleLabel( final String scale_label ) {
4229 _scale_label = scale_label;
4232 final void setSmallFonts() {
4233 getTreeFontSet().smallFonts();
4236 final void setStartingAngle( final double starting_angle ) {
4237 _urt_starting_angle = starting_angle;
4240 final void setSuperTinyFonts() {
4241 getTreeFontSet().superTinyFonts();
4244 final void setTextAntialias() {
4245 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4246 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
4247 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
4250 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
4253 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
4254 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) {
4255 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
4258 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
4261 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
4262 RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
4264 catch ( final Throwable e ) {
4265 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
4269 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
4270 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
4274 final void setTinyFonts() {
4275 getTreeFontSet().tinyFonts();
4279 * Set a phylogeny tree.
4282 * an instance of a Phylogeny
4284 final void setTree( final Phylogeny t ) {
4288 final void setTreeFile( final File treefile ) {
4289 _treefile = treefile;
4292 final private void setUpUrtFactor() {
4293 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4294 : getVisibleRect().height;
4295 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4296 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4299 final int max_depth = _circ_max_depth;
4300 if ( max_depth > 0 ) {
4301 setUrtFactor( d / ( 2 * max_depth ) );
4304 setUrtFactor( d / 2 );
4307 setUrtFactorOv( getUrtFactor() );
4310 final private void setUrtFactor( final float urt_factor ) {
4311 _urt_factor = urt_factor;
4314 final private void setUrtFactorOv( final float urt_factor_ov ) {
4315 _urt_factor_ov = urt_factor_ov;
4318 final void setWaitCursor() {
4319 setCursor( WAIT_CURSOR );
4323 final void setXcorrectionFactor( final float f ) {
4324 _x_correction_factor = f;
4327 final void setXdistance( final float x ) {
4331 final void setYdistance( final float y ) {
4335 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
4337 if ( ( node.getName().length() > 0 )
4338 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
4339 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
4340 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
4341 || node.getBranchData().isHasConfidences() ) {
4342 _popup_buffer.setLength( 0 );
4344 if ( node.getName().length() > 0 ) {
4346 _popup_buffer.append( node.getName() );
4348 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
4350 boolean enc_data = false;
4351 final Taxonomy tax = node.getNodeData().getTaxonomy();
4352 if ( _popup_buffer.length() > 0 ) {
4353 _popup_buffer.append( "\n" );
4355 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
4356 _popup_buffer.append( "[" );
4357 _popup_buffer.append( tax.getTaxonomyCode() );
4358 _popup_buffer.append( "]" );
4361 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
4363 _popup_buffer.append( " " );
4365 _popup_buffer.append( tax.getScientificName() );
4368 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
4370 _popup_buffer.append( " (" );
4373 _popup_buffer.append( "(" );
4375 _popup_buffer.append( tax.getCommonName() );
4376 _popup_buffer.append( ")" );
4379 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
4381 _popup_buffer.append( " (" );
4384 _popup_buffer.append( "(" );
4386 _popup_buffer.append( tax.getAuthority() );
4387 _popup_buffer.append( ")" );
4390 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
4392 _popup_buffer.append( " [" );
4395 _popup_buffer.append( "[" );
4397 _popup_buffer.append( tax.getRank() );
4398 _popup_buffer.append( "]" );
4401 if ( tax.getSynonyms().size() > 0 ) {
4403 _popup_buffer.append( " " );
4405 _popup_buffer.append( "[" );
4407 for( final String syn : tax.getSynonyms() ) {
4408 if ( !ForesterUtil.isEmpty( syn ) ) {
4410 _popup_buffer.append( syn );
4411 if ( counter < tax.getSynonyms().size() ) {
4412 _popup_buffer.append( ", " );
4417 _popup_buffer.append( "]" );
4420 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
4421 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
4422 _popup_buffer.append( "[" );
4423 _popup_buffer.append( tax.getIdentifier().getProvider() );
4424 _popup_buffer.append( "] " );
4426 _popup_buffer.append( tax.getIdentifier().getValue() );
4430 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
4432 boolean enc_data = false;
4433 if ( _popup_buffer.length() > 0 ) {
4434 _popup_buffer.append( "\n" );
4436 final Sequence seq = node.getNodeData().getSequence();
4437 if ( seq.getAccession() != null ) {
4438 _popup_buffer.append( "[" );
4439 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
4440 _popup_buffer.append( seq.getAccession().getSource() );
4441 _popup_buffer.append( ":" );
4443 _popup_buffer.append( seq.getAccession().getValue() );
4444 _popup_buffer.append( "]" );
4447 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
4449 _popup_buffer.append( " [" );
4452 _popup_buffer.append( "[" );
4454 _popup_buffer.append( seq.getSymbol() );
4455 _popup_buffer.append( "]" );
4458 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
4460 _popup_buffer.append( " " );
4462 _popup_buffer.append( seq.getName() );
4465 if ( node.getNodeData().isHasDate() ) {
4467 if ( _popup_buffer.length() > 0 ) {
4468 _popup_buffer.append( "\n" );
4470 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
4472 if ( node.getNodeData().isHasDistribution() ) {
4474 if ( _popup_buffer.length() > 0 ) {
4475 _popup_buffer.append( "\n" );
4477 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
4479 if ( node.getBranchData().isHasConfidences() ) {
4480 final List<Confidence> confs = node.getBranchData().getConfidences();
4481 for( final Confidence confidence : confs ) {
4483 if ( _popup_buffer.length() > 0 ) {
4484 _popup_buffer.append( "\n" );
4486 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
4487 _popup_buffer.append( "[" );
4488 _popup_buffer.append( confidence.getType() );
4489 _popup_buffer.append( "] " );
4491 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil
4492 .round( confidence.getValue(), getOptions()
4493 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
4496 if ( _popup_buffer.length() > 0 ) {
4497 if ( !getConfiguration().isUseNativeUI() ) {
4499 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
4500 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
4501 if ( isInFoundNodes( node ) ) {
4502 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
4504 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4505 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
4508 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
4512 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
4514 _rollover_popup.setText( _popup_buffer.toString() );
4515 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
4517 e.getLocationOnScreen().x + 10,
4518 e.getLocationOnScreen().y
4520 _node_desc_popup.show();
4524 catch ( final Exception ex ) {
4529 final private void showNodeEditFrame( final PhylogenyNode n ) {
4530 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4531 // pop up edit box for single node
4532 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
4533 _node_frame_index++;
4536 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4540 final private void showNodeFrame( final PhylogenyNode n ) {
4541 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4542 // pop up edit box for single node
4543 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
4544 _node_frame_index++;
4547 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4551 final void subTree( final PhylogenyNode node ) {
4552 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4553 JOptionPane.showMessageDialog( this,
4554 "Cannot get a sub/super tree in unrooted display",
4555 "Attempt to get sub/super tree in unrooted display",
4556 JOptionPane.WARNING_MESSAGE );
4559 if ( node.isExternal() ) {
4560 JOptionPane.showMessageDialog( this,
4561 "Cannot get a subtree of a external node",
4562 "Attempt to get subtree of external node",
4563 JOptionPane.WARNING_MESSAGE );
4566 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
4567 JOptionPane.showMessageDialog( this,
4568 "Cannot get a subtree of the root node",
4569 "Attempt to get subtree of root node",
4570 JOptionPane.WARNING_MESSAGE );
4573 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
4574 _sub_phylogenies[ _subtree_index ] = _phylogeny;
4575 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
4577 _phylogeny = subTree( node, _phylogeny );
4578 updateSubSuperTreeButton();
4580 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
4583 _main_panel.getControlPanel().showWhole();
4587 final boolean isCurrentTreeIsSubtree() {
4588 return ( _subtree_index > 0 );
4591 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
4592 final Phylogeny new_phy = new Phylogeny();
4593 new_phy.setRooted( true );
4594 new_phy.setName( source_phy.getName() );
4595 new_phy.setDescription( source_phy.getDescription() );
4596 new_phy.setType( source_phy.getType() );
4597 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
4598 new_phy.setConfidence( source_phy.getConfidence() );
4599 new_phy.setIdentifier( source_phy.getIdentifier() );
4600 new_phy.setRoot( new_root.copyNodeDataShallow() );
4602 for( final PhylogenyNode n : new_root.getDescendants() ) {
4603 new_phy.getRoot().setChildNode( i++, n );
4608 final void superTree() {
4609 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
4610 for( final PhylogenyNode n : temp_root.getDescendants() ) {
4611 n.setParent( temp_root );
4613 _sub_phylogenies[ _subtree_index ] = null;
4614 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
4615 _phylogeny = _sub_phylogenies[ --_subtree_index ];
4616 updateSubSuperTreeButton();
4619 final void swap( final PhylogenyNode node ) {
4620 if ( !node.isExternal() ) {
4621 _phylogeny.swapChildren( node );
4626 final private void switchDisplaygetPhylogenyGraphicsType() {
4627 switch ( getPhylogenyGraphicsType() ) {
4629 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
4630 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
4633 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
4634 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
4637 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
4638 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
4641 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
4642 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
4645 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
4646 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
4649 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
4650 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
4653 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
4654 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
4657 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
4658 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
4661 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
4663 if ( getControlPanel().getDynamicallyHideData() != null ) {
4664 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4665 getControlPanel().getDynamicallyHideData().setEnabled( false );
4668 getControlPanel().getDynamicallyHideData().setEnabled( true );
4671 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
4672 getControlPanel().setDrawPhylogramEnabled( true );
4675 getControlPanel().setDrawPhylogramEnabled( false );
4677 if ( getMainPanel().getMainFrame() == null ) {
4678 // Must be "E" applet version.
4679 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
4680 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
4683 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
4687 final void taxColor() {
4688 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
4692 Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
4693 _control_panel.setColorBranches( true );
4694 if ( _control_panel.getColorBranchesCb() != null ) {
4695 _control_panel.getColorBranchesCb().setSelected( true );
4701 final void updateOvSettings() {
4702 switch ( getOptions().getOvPlacement() ) {
4704 setOvXPosition( OV_BORDER );
4705 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
4706 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
4709 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
4710 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
4711 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
4714 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
4715 setOvYPosition( OV_BORDER );
4716 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
4719 setOvXPosition( OV_BORDER );
4720 setOvYPosition( OV_BORDER );
4721 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
4726 final void updateOvSizes() {
4727 if ( ( getWidth() > 1.05 * getVisibleRect().width ) || ( getHeight() > 1.05 * getVisibleRect().height ) ) {
4729 float l = getLongestExtNodeInfo();
4730 final float w_ratio = getOvMaxWidth() / getWidth();
4732 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
4733 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
4735 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4736 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
4739 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
4741 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
4742 if ( ov_xdist < 0.0 ) {
4745 if ( ydist < 0.0 ) {
4748 setOvXDistance( ov_xdist );
4749 final double height = _phylogeny.getHeight();
4751 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
4752 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
4755 setOvXcorrectionFactor( 0 );
4763 final void updateSubSuperTreeButton() {
4764 if ( _subtree_index < 1 ) {
4765 getControlPanel().deactivateButtonToReturnToSuperTree();
4768 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
4772 final void zoomInDomainStructure() {
4773 if ( _domain_structure_width < 2000 ) {
4774 _domain_structure_width *= 1.2;
4778 final void zoomOutDomainStructure() {
4779 if ( _domain_structure_width > 20 ) {
4780 _domain_structure_width *= 0.8;
4784 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
4785 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
4788 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
4789 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
4792 final private static boolean isSequenceEmpty( final Sequence seq ) {
4793 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
4794 && ForesterUtil.isEmpty( seq.getSymbol() );
4797 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
4798 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
4799 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
4800 .getSynonyms().isEmpty() );
4803 final private static boolean plusPressed( final int key_code ) {
4804 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
4805 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
4808 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
4809 _statistics_for_vector_data = statistics_for_expression_values;
4812 DescriptiveStatistics getStatisticsForExpressionValues() {
4813 return _statistics_for_vector_data;
4816 final private class SubtreeColorizationActionListener implements ActionListener {
4818 JColorChooser _chooser;
4819 PhylogenyNode _node;
4821 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
4827 public void actionPerformed( final ActionEvent e ) {
4828 final Color c = _chooser.getColor();
4830 colorizeSubtree( c, _node );
4835 synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
4836 getMainPanel().setImageMap( image_map );
4839 synchronized Hashtable<String, BufferedImage> getImageMap() {
4840 return getMainPanel().getImageMap();