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.archaeopteryx.tools.Blast;
99 import org.forester.archaeopteryx.tools.ImageLoader;
100 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
101 import org.forester.phylogeny.Phylogeny;
102 import org.forester.phylogeny.PhylogenyMethods;
103 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
104 import org.forester.phylogeny.PhylogenyNode;
105 import org.forester.phylogeny.data.Annotation;
106 import org.forester.phylogeny.data.BranchColor;
107 import org.forester.phylogeny.data.Confidence;
108 import org.forester.phylogeny.data.Event;
109 import org.forester.phylogeny.data.NodeVisualization;
110 import org.forester.phylogeny.data.NodeVisualization.NodeFill;
111 import org.forester.phylogeny.data.NodeVisualization.NodeShape;
112 import org.forester.phylogeny.data.PhylogenyData;
113 import org.forester.phylogeny.data.PhylogenyDataUtil;
114 import org.forester.phylogeny.data.PropertiesMap;
115 import org.forester.phylogeny.data.Property;
116 import org.forester.phylogeny.data.Sequence;
117 import org.forester.phylogeny.data.SequenceRelation;
118 import org.forester.phylogeny.data.Taxonomy;
119 import org.forester.phylogeny.data.Uri;
120 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
121 import org.forester.phylogeny.iterators.PreorderTreeIterator;
122 import org.forester.util.BasicDescriptiveStatistics;
123 import org.forester.util.DescriptiveStatistics;
124 import org.forester.util.ForesterConstants;
125 import org.forester.util.ForesterUtil;
127 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
129 private static final float PI = ( float ) ( Math.PI );
130 private static final double TWO_PI = 2 * Math.PI;
131 private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
132 private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
133 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
134 private static final short OV_BORDER = 10;
135 final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
136 final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
137 final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
138 final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
139 final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
140 private final static long serialVersionUID = -978349745916505029L;
141 private final static int EURO_D = 10;
142 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
143 private final static int MIN_ROOT_LENGTH = 3;
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 LIMIT_FOR_HQ_RENDERING = 1000;
151 private final static int CONFIDENCE_LEFT_MARGIN = 4;
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 PhylogenyNode _root;
212 final private Arc2D _arc = new Arc2D.Double();
213 final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
214 final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
215 final private Set<Integer> _collapsed_external_nodeid_set = new HashSet<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 int _box_size;
224 // private final int _half_box_size;
225 //private final short _skip_counter = 0;
226 private final StringBuffer _popup_buffer = new StringBuffer();
227 final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
230 private static final boolean DRAW_MEAN_COUNTS = true; //TODO remove me later
231 private Sequence _query_sequence = null;
232 private final FontRenderContext _frc = new FontRenderContext( null,
235 // expression values menu:
236 private DescriptiveStatistics _statistics_for_vector_data;
237 private PhylogenyNode[] _nodes_in_preorder = null;
238 // private Image offscreenImage;
239 // private Graphics offscreenGraphics;
240 // private Dimension offscreenDimension;
242 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
243 dfs.setDecimalSeparator( '.' );
244 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
245 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
248 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
249 requestFocusInWindow();
250 addKeyListener( new KeyAdapter() {
253 public void keyPressed( final KeyEvent key_event ) {
254 keyPressedCalls( key_event );
255 requestFocusInWindow();
258 addFocusListener( new FocusAdapter() {
261 public void focusGained( final FocusEvent e ) {
262 requestFocusInWindow();
265 if ( ( t == null ) || t.isEmpty() ) {
266 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
268 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
270 _configuration = configuration;
272 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
274 // if ( !_phylogeny.isEmpty() ) {
275 _phylogeny.recalculateNumberOfExternalDescendants( true );
276 checkForVectorProperties( _phylogeny );
278 setBackground( getTreeColorSet().getBackgroundColor() );
279 final MouseListener mouse_listener = new MouseListener( this );
280 addMouseListener( mouse_listener );
281 addMouseMotionListener( mouse_listener );
282 addMouseWheelListener( this );
283 calculateScaleDistance();
284 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
285 FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
286 .getNumberOfDigitsAfterCommaForBranchLengthValues() );
289 public void checkForVectorProperties( final Phylogeny phy ) {
290 final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
291 for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
292 final PhylogenyNode node = iter.next();
293 if ( node.getNodeData().getProperties() != null ) {
294 final PropertiesMap pm = node.getNodeData().getProperties();
295 final double[] vector = new double[ pm.getProperties().size() ];
297 for( final String ref : pm.getProperties().keySet() ) {
298 if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) {
299 final Property p = pm.getProperty( ref );
300 final String value_str = p.getValue();
301 final String index_str = ref
302 .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() );
305 d = Double.parseDouble( value_str );
307 catch ( final NumberFormatException e ) {
308 JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
309 + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
314 i = Integer.parseInt( index_str );
316 catch ( final NumberFormatException e ) {
317 JOptionPane.showMessageDialog( this,
318 "Could not parse \"" + index_str
319 + "\" into index for vector data",
320 "Problem with Vector Data",
321 JOptionPane.ERROR_MESSAGE );
325 JOptionPane.showMessageDialog( this,
326 "Attempt to use negative index for vector data",
327 "Problem with Vector Data",
328 JOptionPane.ERROR_MESSAGE );
336 final List<Double> vector_l = new ArrayList<Double>( counter );
337 for( int i = 0; i < counter; ++i ) {
338 vector_l.add( vector[ i ] );
340 node.getNodeData().setVector( vector_l );
343 if ( stats.getN() > 0 ) {
344 _statistics_for_vector_data = stats;
348 final public void actionPerformed( final ActionEvent e ) {
349 boolean done = false;
350 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
351 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
352 // NOTE: index corresponds to the indices of click-to options
353 // in the control panel.
354 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
355 // Set this as the new default click-to action
356 _main_panel.getControlPanel().setClickToAction( index );
357 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
358 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
359 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
364 requestFocusInWindow();
367 final private void addEmptyNode( final PhylogenyNode node ) {
368 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
369 errorMessageNoCutCopyPasteInUnrootedDisplay();
372 final String label = getASimpleTextRepresentationOfANode( node );
374 if ( ForesterUtil.isEmpty( label ) ) {
375 msg = "How to add the new, empty node?";
378 msg = "How to add the new, empty node to node" + label + "?";
380 final Object[] options = { "As sibling", "As descendant", "Cancel" };
381 final int r = JOptionPane.showOptionDialog( this,
383 "Addition of Empty New Node",
384 JOptionPane.CLOSED_OPTION,
385 JOptionPane.QUESTION_MESSAGE,
389 boolean add_as_sibling = true;
391 add_as_sibling = false;
396 final Phylogeny phy = new Phylogeny();
397 phy.setRoot( new PhylogenyNode() );
398 phy.setRooted( true );
399 if ( add_as_sibling ) {
400 if ( node.isRoot() ) {
401 JOptionPane.showMessageDialog( this,
402 "Cannot add sibling to root",
403 "Attempt to add sibling to root",
404 JOptionPane.ERROR_MESSAGE );
407 phy.addAsSibling( node );
410 phy.addAsChild( node );
412 setNodeInPreorderToNull();
413 _phylogeny.externalNodesHaveChanged();
414 _phylogeny.clearHashIdToNodeMap();
415 _phylogeny.recalculateNumberOfExternalDescendants( true );
416 resetNodeIdToDistToLeafMap();
421 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
422 final boolean is_vertical,
424 final boolean to_pdf,
425 final boolean to_graphics_file ) {
426 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
427 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
428 g.setColor( Color.BLACK );
430 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
431 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) )
432 && ( getCutOrCopiedTree() != null )
433 && ( getCopiedAndPastedNodes() != null )
435 && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
436 g.setColor( getTreeColorSet().getFoundColor() );
438 else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
439 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
442 g.setColor( getTreeColorSet().getBranchColorForPdf() );
445 g.setColor( getTreeColorSet().getBranchColor() );
449 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
450 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
451 return ( PhylogenyMethods.getBranchColorValue( node ) );
454 return ( getTreeColorSet().getBranchColor() );
458 final private void blast( final PhylogenyNode node ) {
459 if ( !isCanBlast( node ) ) {
460 JOptionPane.showMessageDialog( this,
461 "No sequence information present",
463 JOptionPane.WARNING_MESSAGE );
466 if ( node.getNodeData().isHasSequence() ) {
467 final String query = Blast.obtainQueryForBlast( node );
468 boolean nucleotide = false;
469 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
470 if ( !node.getNodeData().getSequence().getType().toLowerCase().equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
474 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
475 nucleotide = !ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() );
477 if ( !ForesterUtil.isEmpty( query ) ) {
478 JApplet applet = null;
480 applet = obtainApplet();
483 Blast.openNcbiBlastWeb( query, nucleotide, applet, this );
485 catch ( final Exception e ) {
488 if ( Constants.ALLOW_DDBJ_BLAST ) {
490 System.out.println( "trying: " + query );
491 final Blast s = new Blast();
492 s.ddbjBlast( query );
494 catch ( final Exception e ) {
502 final void calcMaxDepth() {
503 if ( _phylogeny != null ) {
504 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
509 * Calculate the length of the distance between the given node and its
515 * @return the distance value
517 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
518 if ( getControlPanel().isDrawPhylogram() ) {
519 if ( node.getDistanceToParent() < 0.0 ) {
522 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
525 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
526 return getXdistance();
528 return getXdistance() * factor;
532 final private Color calculateColorForAnnotation( final PhylogenyData ann ) {
533 Color c = getTreeColorSet().getAnnotationColor();
534 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
535 c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() );
537 c = getTreeColorSet().getAnnotationColor();
543 final void calculateLongestExtNodeInfo() {
544 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
547 int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
548 * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
549 if ( max_length < 40 ) {
553 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
555 if ( node.isCollapse() ) {
558 if ( getControlPanel().isShowNodeNames() ) {
559 sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
561 if ( node.getNodeData().isHasSequence() ) {
562 if ( getControlPanel().isShowSequenceAcc()
563 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
564 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
568 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
569 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
571 if ( getControlPanel().isShowGeneSymbols()
572 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
573 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
575 if ( getControlPanel().isShowAnnotation()
576 && ( node.getNodeData().getSequence().getAnnotations() != null )
577 && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
578 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
582 if ( getControlPanel().isShowDomainArchitectures()
583 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
584 sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
585 .getRenderingSize().getWidth();
588 if ( node.getNodeData().isHasTaxonomy() ) {
589 final Taxonomy tax = node.getNodeData().getTaxonomy();
590 if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
591 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
593 if ( getControlPanel().isShowTaxonomyScientificNames()
594 && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
595 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
597 if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
598 sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
601 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
602 sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
604 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
605 sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
606 .getGainedCharactersAsStringBuffer().toString() );
608 if ( sum >= max_length ) {
609 setLongestExtNodeInfo( max_length );
612 if ( sum > longest ) {
616 if ( longest >= max_length ) {
617 setLongestExtNodeInfo( max_length );
620 setLongestExtNodeInfo( longest );
624 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
625 if ( getControlPanel().isDrawPhylogram() ) {
626 if ( node.getDistanceToParent() < 0.0 ) {
629 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
632 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
633 return getOvXDistance();
635 return getOvXDistance() * factor;
639 final void calculateScaleDistance() {
640 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
643 final double height = getMaxDistanceToRoot();
645 if ( ( height <= 0.5 ) ) {
646 setScaleDistance( 0.01 );
648 else if ( height <= 5.0 ) {
649 setScaleDistance( 0.1 );
651 else if ( height <= 50.0 ) {
652 setScaleDistance( 1 );
654 else if ( height <= 500.0 ) {
655 setScaleDistance( 10 );
658 setScaleDistance( 100 );
662 setScaleDistance( 0.0 );
664 String scale_label = String.valueOf( getScaleDistance() );
665 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
666 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
668 setScaleLabel( scale_label );
671 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
672 String species = tax.getTaxonomyCode();
673 if ( ForesterUtil.isEmpty( species ) ) {
674 species = tax.getScientificName();
675 if ( ForesterUtil.isEmpty( species ) ) {
676 species = tax.getCommonName();
679 if ( ForesterUtil.isEmpty( species ) ) {
680 return getTreeColorSet().getTaxonomyColor();
682 // Look in species hash
683 Color c = getControlPanel().getSpeciesColors().get( species );
685 c = AptxUtil.calculateColorFromString( species );
686 getControlPanel().getSpeciesColors().put( species, c );
691 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
692 JOptionPane.showMessageDialog( this,
693 "Cannot launch web browser for " + type_type + " data of this node",
694 "Cannot launch web browser",
695 JOptionPane.WARNING_MESSAGE );
699 * Collapse the tree from the given node
704 final void collapse( final PhylogenyNode node ) {
705 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
706 JOptionPane.showMessageDialog( this,
707 "Cannot collapse in unrooted display type",
708 "Attempt to collapse in unrooted display",
709 JOptionPane.WARNING_MESSAGE );
712 if ( !node.isExternal() && !node.isRoot() ) {
713 final boolean collapse = !node.isCollapse();
714 AptxUtil.collapseSubtree( node, collapse );
715 updateSetOfCollapsedExternalNodes();
716 _phylogeny.recalculateNumberOfExternalDescendants( true );
717 resetNodeIdToDistToLeafMap();
718 calculateLongestExtNodeInfo();
719 setNodeInPreorderToNull();
720 _control_panel.displayedPhylogenyMightHaveChanged( true );
721 resetPreferredSize();
723 _main_panel.adjustJScrollPane();
728 final void collapseSpeciesSpecificSubtrees() {
729 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
733 AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
734 updateSetOfCollapsedExternalNodes();
735 _phylogeny.recalculateNumberOfExternalDescendants( true );
736 resetNodeIdToDistToLeafMap();
737 calculateLongestExtNodeInfo();
738 setNodeInPreorderToNull();
739 resetPreferredSize();
740 _main_panel.adjustJScrollPane();
745 final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
746 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
747 JOptionPane.showMessageDialog( this,
748 "Cannot colorize subtree in unrooted display type",
749 "Attempt to colorize subtree in unrooted display",
750 JOptionPane.WARNING_MESSAGE );
753 _control_panel.setColorBranches( true );
754 if ( _control_panel.getColorBranchesCb() != null ) {
755 _control_panel.getColorBranchesCb().setSelected( true );
757 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
758 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
763 final private void colorSubtree( final PhylogenyNode node ) {
764 Color intitial_color = null;
765 if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
766 && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
767 intitial_color = PhylogenyMethods.getBranchColorValue( node );
770 intitial_color = getTreeColorSet().getBranchColor();
772 _color_chooser.setColor( intitial_color );
773 _color_chooser.setPreviewPanel( new JPanel() );
774 final JDialog dialog = JColorChooser
776 "Subtree colorization",
779 new SubtreeColorizationActionListener( _color_chooser, node ),
781 dialog.setVisible( true );
784 final void confColor() {
785 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
789 AptxUtil.removeBranchColors( _phylogeny );
790 AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
791 _control_panel.setColorBranches( true );
792 if ( _control_panel.getColorBranchesCb() != null ) {
793 _control_panel.getColorBranchesCb().setSelected( true );
799 final void colorRank( final String rank ) {
800 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
804 AptxUtil.removeBranchColors( _phylogeny );
805 final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
806 if ( colorizations > 0 ) {
807 _control_panel.setColorBranches( true );
808 if ( _control_panel.getColorBranchesCb() != null ) {
809 _control_panel.getColorBranchesCb().setSelected( true );
811 if ( _control_panel.getColorAccSpeciesCb() != null ) {
812 _control_panel.getColorAccSpeciesCb().setSelected( false );
814 _options.setColorLabelsSameAsParentBranch( true );
815 _control_panel.repaint();
819 if ( colorizations > 0 ) {
820 String msg = "Taxonomy colorization via " + rank + " completed:\n";
821 if ( colorizations > 1 ) {
822 msg += "colorized " + colorizations + " subtrees";
825 msg += "colorized one subtree";
827 JOptionPane.showMessageDialog( this,
829 "Taxonomy Colorization Completed (" + rank + ")",
830 JOptionPane.INFORMATION_MESSAGE );
833 String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
834 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
835 msg += "select a different rank (e.g. phylum, genus, ...)\n";
838 msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
839 msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
840 JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
844 final private void copySubtree( final PhylogenyNode node ) {
845 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
846 errorMessageNoCutCopyPasteInUnrootedDisplay();
849 setNodeInPreorderToNull();
850 setCutOrCopiedTree( _phylogeny.copy( node ) );
851 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
852 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
853 for( final PhylogenyNode n : nodes ) {
854 node_ids.add( n.getId() );
856 node_ids.add( node.getId() );
857 setCopiedAndPastedNodes( node_ids );
861 final private void cutSubtree( final PhylogenyNode node ) {
862 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
863 errorMessageNoCutCopyPasteInUnrootedDisplay();
866 if ( node.isRoot() ) {
867 JOptionPane.showMessageDialog( this,
868 "Cannot cut entire tree as subtree",
869 "Attempt to cut entire tree",
870 JOptionPane.ERROR_MESSAGE );
873 final String label = getASimpleTextRepresentationOfANode( node );
874 final int r = JOptionPane.showConfirmDialog( null,
875 "Cut subtree" + label + "?",
876 "Confirm Cutting of Subtree",
877 JOptionPane.YES_NO_OPTION );
878 if ( r != JOptionPane.OK_OPTION ) {
881 setNodeInPreorderToNull();
882 setCopiedAndPastedNodes( null );
883 setCutOrCopiedTree( _phylogeny.copy( node ) );
884 _phylogeny.deleteSubtree( node, true );
885 _phylogeny.clearHashIdToNodeMap();
886 _phylogeny.recalculateNumberOfExternalDescendants( true );
887 resetNodeIdToDistToLeafMap();
892 final private void cycleColors() {
893 getMainPanel().getTreeColorSet().cycleColorScheme();
894 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
895 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
899 final void decreaseDomainStructureEvalueThreshold() {
900 if ( _domain_structure_e_value_thr_exp > -20 ) {
901 _domain_structure_e_value_thr_exp -= 1;
905 final private void decreaseOvSize() {
906 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
907 setOvMaxWidth( getOvMaxWidth() - 5 );
908 setOvMaxHeight( getOvMaxHeight() - 5 );
910 getControlPanel().displayedPhylogenyMightHaveChanged( false );
914 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
915 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
916 errorMessageNoCutCopyPasteInUnrootedDisplay();
919 if ( node.isRoot() ) {
920 JOptionPane.showMessageDialog( this,
921 "Cannot delete entire tree",
922 "Attempt to delete entire tree",
923 JOptionPane.ERROR_MESSAGE );
926 final String label = getASimpleTextRepresentationOfANode( node );
927 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
928 final int r = JOptionPane.showOptionDialog( this,
929 "Delete" + label + "?",
930 "Delete Node/Subtree",
931 JOptionPane.CLOSED_OPTION,
932 JOptionPane.QUESTION_MESSAGE,
936 setNodeInPreorderToNull();
937 boolean node_only = true;
945 PhylogenyMethods.removeNode( node, _phylogeny );
948 _phylogeny.deleteSubtree( node, true );
950 _phylogeny.externalNodesHaveChanged();
951 _phylogeny.clearHashIdToNodeMap();
952 _phylogeny.recalculateNumberOfExternalDescendants( true );
953 resetNodeIdToDistToLeafMap();
958 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
959 makePopupMenus( node );
960 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
961 _node_popup_menu.show( this, x, y );
964 final private void drawArc( final double x,
968 final double start_angle,
969 final double arc_angle,
970 final Graphics2D g ) {
971 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
975 final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) {
976 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
979 _line.setLine( x1, y1, x2, y2 );
983 final private void drawOval( final double x,
987 final Graphics2D g ) {
988 _ellipse.setFrame( x, y, width, heigth );
992 final private void drawOvalFilled( final double x,
996 final Graphics2D g ) {
997 _ellipse.setFrame( x, y, width, heigth );
1001 final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) {
1002 _rectangle.setFrame( x, y, width, heigth );
1003 g.draw( _rectangle );
1006 final private void drawRectFilled( final double x,
1009 final double heigth,
1010 final Graphics2D g ) {
1011 _rectangle.setFrame( x, y, width, heigth );
1012 g.fill( _rectangle );
1015 final private void drawRectGradient( final double x,
1018 final double heigth,
1020 final Color color_1,
1021 final Color color_2,
1022 final Color color_border ) {
1023 _rectangle.setFrame( x, y, width, heigth );
1024 g.setPaint( new GradientPaint( ( float ) x,
1027 ( float ) ( x + width ),
1028 ( float ) ( y + heigth ),
1031 g.fill( _rectangle );
1032 if ( color_border != null ) {
1033 g.setPaint( color_border );
1034 g.draw( _rectangle );
1038 final private void drawOvalGradient( final double x,
1041 final double heigth,
1043 final Color color_1,
1044 final Color color_2,
1045 final Color color_border ) {
1046 _ellipse.setFrame( x, y, width, heigth );
1047 g.setPaint( new GradientPaint( ( float ) x,
1050 ( float ) ( x + width ),
1051 ( float ) ( y + heigth ),
1055 if ( color_border != null ) {
1056 g.setPaint( color_border );
1061 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
1062 JOptionPane.showMessageDialog( this,
1063 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
1064 "Attempt to cut/copy/paste/add/delete in unrooted display",
1065 JOptionPane.ERROR_MESSAGE );
1069 * Find the node, if any, at the given location
1073 * @return pointer to the node at x,y, null if not found
1075 final PhylogenyNode findNode( final int x, final int y ) {
1076 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1079 final int half_box_size_plus_wiggle = getOptions().getDefaultNodeShapeSize() / 2 + WIGGLE;
1080 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
1081 final PhylogenyNode node = iter.next();
1082 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
1083 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
1084 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
1085 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
1086 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
1093 final private String getASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
1094 final String tax = PhylogenyMethods.getSpecies( node );
1095 String label = node.getName();
1096 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
1097 label = label + " " + tax;
1099 else if ( !ForesterUtil.isEmpty( tax ) ) {
1105 if ( !ForesterUtil.isEmpty( label ) ) {
1106 label = " [" + label + "]";
1111 final Configuration getConfiguration() {
1112 return _configuration;
1115 final ControlPanel getControlPanel() {
1116 return _control_panel;
1119 final private Set<Integer> getCopiedAndPastedNodes() {
1120 return getMainPanel().getCopiedAndPastedNodes();
1123 final private Phylogeny getCutOrCopiedTree() {
1124 return getMainPanel().getCutOrCopiedTree();
1127 final int getDomainStructureEvalueThreshold() {
1128 return _domain_structure_e_value_thr_exp;
1131 final Set<Integer> getFoundNodes() {
1132 return _found_nodes;
1135 final private float getLastDragPointX() {
1136 return _last_drag_point_x;
1139 final private float getLastDragPointY() {
1140 return _last_drag_point_y;
1143 final int getLongestExtNodeInfo() {
1144 return _longest_ext_node_info;
1147 final public MainPanel getMainPanel() {
1151 final private short getMaxBranchesToLeaf( final PhylogenyNode node ) {
1152 if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) {
1153 final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node );
1154 _nodeid_dist_to_leaf.put( node.getId(), m );
1158 return _nodeid_dist_to_leaf.get( node.getId() );
1162 final private double getMaxDistanceToRoot() {
1163 if ( _max_distance_to_root < 0 ) {
1164 recalculateMaxDistanceToRoot();
1166 return _max_distance_to_root;
1169 final Options getOptions() {
1170 if ( _options == null ) {
1171 _options = getControlPanel().getOptions();
1176 final private float getOvMaxHeight() {
1177 return _ov_max_height;
1180 final private float getOvMaxWidth() {
1181 return _ov_max_width;
1184 final Rectangle2D getOvRectangle() {
1185 return _ov_rectangle;
1188 final Rectangle getOvVirtualRectangle() {
1189 return _ov_virtual_rectangle;
1192 final private float getOvXcorrectionFactor() {
1193 return _ov_x_correction_factor;
1196 final private float getOvXDistance() {
1197 return _ov_x_distance;
1200 final private int getOvXPosition() {
1201 return _ov_x_position;
1204 final private float getOvYDistance() {
1205 return _ov_y_distance;
1208 final private int getOvYPosition() {
1209 return _ov_y_position;
1212 final private int getOvYStart() {
1217 * Get a pointer to the phylogeny
1219 * @return a pointer to the phylogeny
1221 public final Phylogeny getPhylogeny() {
1225 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
1226 return _graphics_type;
1229 final private double getScaleDistance() {
1230 return _scale_distance;
1233 final private String getScaleLabel() {
1234 return _scale_label;
1237 final double getStartingAngle() {
1238 return _urt_starting_angle;
1242 * Find a color for this species name.
1245 * @return the species color
1247 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
1248 if ( node.getNodeData().isHasTaxonomy() ) {
1249 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
1251 // return non-colorized color
1252 return getTreeColorSet().getTaxonomyColor();
1256 * @return pointer to colorset for tree drawing
1258 final TreeColorSet getTreeColorSet() {
1259 return getMainPanel().getTreeColorSet();
1262 final File getTreeFile() {
1266 final private TreeFontSet getTreeFontSet() {
1267 return getMainPanel().getTreeFontSet();
1270 final private float getUrtFactor() {
1274 final private float getUrtFactorOv() {
1275 return _urt_factor_ov;
1278 final float getXcorrectionFactor() {
1279 return _x_correction_factor;
1282 final float getXdistance() {
1286 final float getYdistance() {
1290 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
1293 showNodeFrame( node );
1308 colorSubtree( node );
1323 copySubtree( node );
1326 pasteSubtree( node );
1328 case DELETE_NODE_OR_SUBTREE:
1329 deleteNodeOrSubtree( node );
1332 addEmptyNode( node );
1334 case EDIT_NODE_DATA:
1335 showNodeEditFrame( node );
1337 case SORT_DESCENDENTS:
1338 sortDescendants( node );
1340 case GET_EXT_DESC_DATA:
1341 getExtDescNodeData( node );
1344 throw new IllegalArgumentException( "unknown action: " + action );
1348 private void getExtDescNodeData( final PhylogenyNode node ) {
1349 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
1350 switch ( getOptions().getExtDescNodeDataToReturn() ) {
1352 System.out.println( n.getName() );
1355 if ( n.getNodeData().isHasSequence()
1356 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
1357 System.out.println( n.getNodeData().getSequence().getName() );
1360 case SEQUENCE_SYMBOL:
1361 if ( n.getNodeData().isHasSequence()
1362 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
1363 System.out.println( n.getNodeData().getSequence().getSymbol() );
1366 case SEQUENCE_MOL_SEQ:
1367 if ( n.getNodeData().isHasSequence()
1368 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
1369 System.out.println( n.getNodeData().getSequence().getMolecularSequence() );
1373 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null ) ) {
1374 System.out.println( n.getNodeData().getSequence().getAccession().toString() );
1378 throw new IllegalArgumentException( "unknown data element: "
1379 + getOptions().getExtDescNodeDataToReturn() );
1384 final void increaseDomainStructureEvalueThreshold() {
1385 if ( _domain_structure_e_value_thr_exp < 3 ) {
1386 _domain_structure_e_value_thr_exp += 1;
1390 final private void increaseOvSize() {
1391 if ( ( getOvMaxWidth() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 )
1392 && ( getOvMaxHeight() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
1393 .getHeight() / 2 ) ) {
1394 setOvMaxWidth( getOvMaxWidth() + 5 );
1395 setOvMaxHeight( getOvMaxHeight() + 5 );
1397 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1401 final void inferCommonPartOfScientificNames() {
1402 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1406 AptxUtil.inferCommonPartOfScientificNames( _phylogeny );
1411 final private void init() {
1412 _color_chooser = new JColorChooser();
1413 _rollover_popup = new JTextArea();
1414 _rollover_popup.setFont( POPUP_FONT );
1415 resetNodeIdToDistToLeafMap();
1417 setTreeFile( null );
1419 initializeOvSettings();
1420 setStartingAngle( TWO_PI * 3 / 4 );
1421 final ImageLoader il = new ImageLoader( this );
1422 new Thread( il ).start();
1425 final private void initializeOvSettings() {
1426 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
1427 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
1430 final void initNodeData() {
1431 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1434 double max_original_domain_structure_width = 0.0;
1435 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1436 if ( node.getNodeData().isHasSequence()
1437 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1438 RenderableDomainArchitecture rds = null;
1439 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1440 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1441 getConfiguration() );
1442 node.getNodeData().getSequence().setDomainArchitecture( rds );
1445 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1447 if ( getControlPanel().isShowDomainArchitectures() ) {
1448 final double dsw = rds.getOriginalSize().getWidth();
1449 if ( dsw > max_original_domain_structure_width ) {
1450 max_original_domain_structure_width = dsw;
1455 if ( getControlPanel().isShowDomainArchitectures() ) {
1456 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1457 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1458 if ( node.getNodeData().isHasSequence()
1459 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1460 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1461 .getSequence().getDomainArchitecture();
1462 rds.setRenderingFactorWidth( ds_factor_width );
1463 rds.setParameter( _domain_structure_e_value_thr_exp );
1469 final boolean inOv( final MouseEvent e ) {
1470 return ( ( e.getX() > getVisibleRect().x + getOvXPosition() + 1 )
1471 && ( e.getX() < getVisibleRect().x + getOvXPosition() + getOvMaxWidth() - 1 )
1472 && ( e.getY() > getVisibleRect().y + getOvYPosition() + 1 ) && ( e.getY() < getVisibleRect().y
1473 + getOvYPosition() + getOvMaxHeight() - 1 ) );
1476 final boolean inOvRectangle( final MouseEvent e ) {
1477 return ( ( e.getX() >= getOvRectangle().getX() - 1 )
1478 && ( e.getX() <= getOvRectangle().getX() + getOvRectangle().getWidth() + 1 )
1479 && ( e.getY() >= getOvRectangle().getY() - 1 ) && ( e.getY() <= getOvRectangle().getY()
1480 + getOvRectangle().getHeight() + 1 ) );
1483 final private boolean inOvVirtualRectangle( final int x, final int y ) {
1484 return ( ( x >= getOvVirtualRectangle().x - 1 )
1485 && ( x <= getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 )
1486 && ( y >= getOvVirtualRectangle().y - 1 ) && ( y <= getOvVirtualRectangle().y
1487 + getOvVirtualRectangle().height + 1 ) );
1490 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
1491 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
1494 final boolean isApplet() {
1495 return getMainPanel() instanceof MainPanelApplets;
1498 final private boolean isCanBlast( final PhylogenyNode node ) {
1499 return ( node.getNodeData().isHasSequence()
1500 && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil.isEmpty( node
1501 .getNodeData().getSequence().getAccession().getValue() ) )
1502 || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil
1503 .isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) && Blast
1504 .isContainsQueryForBlast( node ) );
1507 final boolean isCanCollapse() {
1508 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1511 final boolean isCanColorSubtree() {
1512 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1515 final boolean isCanCopy() {
1516 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1519 final boolean isCanCut( final PhylogenyNode node ) {
1520 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1524 final boolean isCanDelete() {
1525 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1528 final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
1529 if ( node.getNodeData().isHasSequence()
1530 && ( node.getNodeData().getSequence().getAccession() != null )
1531 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
1532 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
1533 && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
1534 .toLowerCase() ) ) {
1540 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
1541 if ( node.getNodeData().isHasTaxonomy()
1542 && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
1543 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
1544 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
1545 .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
1546 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
1547 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
1548 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
1549 .getNodeData().getTaxonomy().getIdentifier() != null )
1550 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
1551 .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
1559 final boolean isCanPaste() {
1560 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1561 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1564 final boolean isCanReroot() {
1565 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1568 final boolean isCanSubtree( final PhylogenyNode node ) {
1569 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1570 .isRoot() || ( _subtree_index > 0 ) ) );
1573 final boolean isEdited() {
1577 final private boolean isInFoundNodes( final PhylogenyNode node ) {
1578 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
1581 final private boolean isInOv() {
1585 final boolean isInOvRect() {
1589 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
1591 if ( getControlPanel().isShowTaxonomyImages() ) {
1592 y_dist = 40 + ( int ) getYdistance();
1594 return ( ( node.getYcoord() < getVisibleRect().getMinY() - y_dist )
1595 || ( node.getYcoord() > getVisibleRect().getMaxY() + y_dist ) || ( ( node.getParent() != null ) && ( node
1596 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
1599 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
1600 return ( ( node.getYcoord() < getVisibleRect().getMinY() - 20 )
1601 || ( node.getYcoord() > getVisibleRect().getMaxY() + 20 )
1602 || ( node.getXcoord() < getVisibleRect().getMinX() - 20 ) || ( node.getXcoord() > getVisibleRect()
1603 .getMaxX() + 20 ) );
1606 final private boolean isNonLinedUpCladogram() {
1607 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
1610 final boolean isOvOn() {
1614 final boolean isPhyHasBranchLengths() {
1615 return _phy_has_branch_lengths;
1618 final private boolean isUniformBranchLengthsForCladogram() {
1619 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
1622 final private void keyPressedCalls( final KeyEvent e ) {
1623 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
1624 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
1625 if ( !isInOvRect() ) {
1626 setInOvRect( true );
1629 else if ( isInOvRect() ) {
1630 setInOvRect( false );
1633 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
1634 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1635 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
1636 getMainPanel().getTreeFontSet().mediumFonts();
1637 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1639 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1640 getMainPanel().getTreeFontSet().decreaseFontSize();
1641 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1643 else if ( plusPressed( e.getKeyCode() ) ) {
1644 getMainPanel().getTreeFontSet().increaseFontSize();
1645 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1649 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1650 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
1651 getControlPanel().showWhole();
1653 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
1654 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
1655 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
1656 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
1657 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1658 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1660 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1661 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1662 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1664 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1665 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1666 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1667 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1669 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1670 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1671 Constants.WHEEL_ZOOM_IN_FACTOR );
1672 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1679 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1682 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1686 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1690 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1691 scroll_position.x = scroll_position.x + dx;
1692 scroll_position.y = scroll_position.y + dy;
1693 if ( scroll_position.x <= 0 ) {
1694 scroll_position.x = 0;
1697 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1698 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1699 if ( scroll_position.x >= max_x ) {
1700 scroll_position.x = max_x;
1703 if ( scroll_position.y <= 0 ) {
1704 scroll_position.y = 0;
1707 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1708 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1709 if ( scroll_position.y >= max_y ) {
1710 scroll_position.y = max_y;
1714 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1717 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1718 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1719 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1720 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1721 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1723 else if ( plusPressed( e.getKeyCode() ) ) {
1724 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1725 Constants.WHEEL_ZOOM_IN_FACTOR );
1726 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1727 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1729 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
1730 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1731 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1732 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
1733 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1736 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
1737 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1738 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1739 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
1740 if ( getStartingAngle() < 0 ) {
1741 setStartingAngle( TWO_PI + getStartingAngle() );
1743 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1746 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
1747 boolean selected = false;
1748 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
1749 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1753 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1755 if ( getMainPanel().getMainFrame() == null ) {
1756 // Must be "E" applet version.
1757 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1758 if ( ae.getlabelDirectionCbmi() != null ) {
1759 ae.getlabelDirectionCbmi().setSelected( selected );
1763 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
1767 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
1768 switchDisplaygetPhylogenyGraphicsType();
1771 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
1775 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
1776 MainFrame.cycleOverview( getOptions(), this );
1779 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
1782 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
1789 final private void makePopupMenus( final PhylogenyNode node ) {
1790 _node_popup_menu = new JPopupMenu();
1791 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
1792 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
1793 for( int i = 0; i < clickto_names.size(); i++ ) {
1794 final String title = clickto_names.get( i );
1795 _node_popup_menu_items[ i ] = new JMenuItem( title );
1796 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
1797 _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
1799 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
1800 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
1802 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
1803 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
1805 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
1806 if ( !getOptions().isEditable() ) {
1809 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
1811 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
1812 if ( !getOptions().isEditable() ) {
1815 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
1817 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
1818 if ( !getOptions().isEditable() ) {
1821 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
1823 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
1824 if ( !getOptions().isEditable() ) {
1827 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
1829 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
1830 if ( !getOptions().isEditable() ) {
1834 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
1835 if ( !getOptions().isEditable() ) {
1839 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
1840 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
1842 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
1843 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
1845 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
1846 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
1848 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
1849 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
1851 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
1852 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
1854 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
1855 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
1857 _node_popup_menu_items[ i ].addActionListener( this );
1858 _node_popup_menu.add( _node_popup_menu_items[ i ] );
1862 final void midpointRoot() {
1863 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1866 if ( !_phylogeny.isRerootable() ) {
1867 JOptionPane.showMessageDialog( this,
1868 "This is not rerootable",
1870 JOptionPane.WARNING_MESSAGE );
1873 setNodeInPreorderToNull();
1875 PhylogenyMethods.midpointRoot( _phylogeny );
1876 resetNodeIdToDistToLeafMap();
1881 final void mouseClicked( final MouseEvent e ) {
1882 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1883 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1884 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1885 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - getOvRectangle().getWidth() / 2.0 )
1887 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - getOvRectangle().getHeight() / 2.0 )
1895 final double max_x = getWidth() - getVisibleRect().width;
1896 final double max_y = getHeight() - getVisibleRect().height;
1903 getMainPanel().getCurrentScrollPane().getViewport()
1904 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1905 setInOvRect( true );
1909 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1910 if ( node != null ) {
1911 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1914 _highlight_node = node;
1915 // Check if shift key is down
1916 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1917 // Yes, so add to _found_nodes
1918 if ( getFoundNodes() == null ) {
1919 setFoundNodes( new HashSet<Integer>() );
1921 getFoundNodes().add( node.getId() );
1922 // Check if control key is down
1924 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1925 // Yes, so pop-up menu
1926 displayNodePopupMenu( node, e.getX(), e.getY() );
1927 // Handle unadorned click
1930 // Check for right mouse button
1931 if ( e.getModifiers() == 4 ) {
1932 displayNodePopupMenu( node, e.getX(), e.getY() );
1935 // if not in _found_nodes, clear _found_nodes
1936 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1941 // no node was clicked
1942 _highlight_node = null;
1948 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1949 setCursor( MOVE_CURSOR );
1950 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1951 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1952 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1953 if ( scroll_position.x < 0 ) {
1954 scroll_position.x = 0;
1957 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1958 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1959 if ( scroll_position.x > max_x ) {
1960 scroll_position.x = max_x;
1963 if ( scroll_position.y < 0 ) {
1964 scroll_position.y = 0;
1967 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1968 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1969 if ( scroll_position.y > max_y ) {
1970 scroll_position.y = max_y;
1973 if ( isOvOn() || getOptions().isShowScale() ) {
1976 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1979 final void mouseDragInOvRectangle( final MouseEvent e ) {
1980 setCursor( HAND_CURSOR );
1981 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1982 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1983 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1984 double dx = ( w_ratio * e.getX() - w_ratio * getLastDragPointX() );
1985 double dy = ( h_ratio * e.getY() - h_ratio * getLastDragPointY() );
1986 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1987 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1988 if ( scroll_position.x <= 0 ) {
1989 scroll_position.x = 0;
1993 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1994 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1995 if ( scroll_position.x >= max_x ) {
1997 scroll_position.x = max_x;
2000 if ( scroll_position.y <= 0 ) {
2002 scroll_position.y = 0;
2005 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
2006 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
2007 if ( scroll_position.y >= max_y ) {
2009 scroll_position.y = max_y;
2013 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
2014 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
2015 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
2018 final void mouseMoved( final MouseEvent e ) {
2019 requestFocusInWindow();
2020 if ( getControlPanel().isNodeDescPopup() ) {
2021 if ( _node_desc_popup != null ) {
2022 _node_desc_popup.hide();
2023 _node_desc_popup = null;
2026 if ( getOptions().isShowOverview() && isOvOn() ) {
2027 if ( inOvVirtualRectangle( e ) ) {
2028 if ( !isInOvRect() ) {
2029 setInOvRect( true );
2034 if ( isInOvRect() ) {
2035 setInOvRect( false );
2040 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
2049 final PhylogenyNode node = findNode( e.getX(), e.getY() );
2050 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
2051 // cursor is over a tree node
2052 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
2053 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
2054 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
2055 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
2056 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
2057 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
2058 setCursor( CUT_CURSOR );
2061 setCursor( HAND_CURSOR );
2062 if ( getControlPanel().isNodeDescPopup() ) {
2063 showNodeDataPopup( e, node );
2068 setCursor( ARROW_CURSOR );
2073 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
2074 setCursor( ARROW_CURSOR );
2077 final public void mouseWheelMoved( final MouseWheelEvent e ) {
2078 final int notches = e.getWheelRotation();
2079 if ( inOvVirtualRectangle( e ) ) {
2080 if ( !isInOvRect() ) {
2081 setInOvRect( true );
2086 if ( isInOvRect() ) {
2087 setInOvRect( false );
2091 if ( e.isControlDown() ) {
2092 if ( notches < 0 ) {
2093 getTreeFontSet().increaseFontSize();
2094 getControlPanel().displayedPhylogenyMightHaveChanged( true );
2097 getTreeFontSet().decreaseFontSize();
2098 getControlPanel().displayedPhylogenyMightHaveChanged( true );
2101 else if ( e.isShiftDown() ) {
2102 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
2103 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
2104 if ( notches < 0 ) {
2105 for( int i = 0; i < ( -notches ); ++i ) {
2106 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
2107 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2111 for( int i = 0; i < notches; ++i ) {
2112 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
2113 if ( getStartingAngle() < 0 ) {
2114 setStartingAngle( TWO_PI + getStartingAngle() );
2116 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2121 if ( notches < 0 ) {
2122 for( int i = 0; i < ( -notches ); ++i ) {
2123 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
2124 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2128 for( int i = 0; i < notches; ++i ) {
2129 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
2130 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2136 if ( notches < 0 ) {
2137 for( int i = 0; i < ( -notches ); ++i ) {
2138 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
2139 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
2140 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
2141 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2145 for( int i = 0; i < notches; ++i ) {
2146 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
2147 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
2148 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
2149 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2154 requestFocusInWindow();
2158 final void multiplyUrtFactor( final float f ) {
2162 final JApplet obtainApplet() {
2163 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
2166 final private void openSeqWeb( final PhylogenyNode node ) {
2167 if ( !isCanOpenSeqWeb( node ) ) {
2168 cannotOpenBrowserWarningMessage( "sequence" );
2171 String uri_str = null;
2172 final Sequence seq = node.getNodeData().getSequence();
2173 final String source = seq.getAccession().getSource().toLowerCase();
2175 if ( source.toLowerCase().equals( "ncbi" ) ) {
2176 url = Constants.NCBI_ALL_DATABASE_SEARCH;
2179 final WebLink weblink = getConfiguration().getWebLink( source );
2180 url = weblink.getUrl().toString();
2183 uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
2185 catch ( final UnsupportedEncodingException e ) {
2186 AptxUtil.showErrorMessage( this, e.toString() );
2187 e.printStackTrace();
2189 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2191 JApplet applet = null;
2193 applet = obtainApplet();
2195 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
2197 catch ( final IOException e ) {
2198 AptxUtil.showErrorMessage( this, e.toString() );
2199 e.printStackTrace();
2201 catch ( final URISyntaxException e ) {
2202 AptxUtil.showErrorMessage( this, e.toString() );
2203 e.printStackTrace();
2207 cannotOpenBrowserWarningMessage( "sequence" );
2211 final private void openTaxWeb( final PhylogenyNode node ) {
2212 if ( !isCanOpenTaxWeb( node ) ) {
2213 cannotOpenBrowserWarningMessage( "taxonomic" );
2216 String uri_str = null;
2217 final Taxonomy tax = node.getNodeData().getTaxonomy();
2218 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
2219 && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
2220 final String type = tax.getIdentifier().getProvider().toLowerCase();
2221 final WebLink weblink = getConfiguration().getWebLink( type );
2223 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
2225 catch ( final UnsupportedEncodingException e ) {
2226 AptxUtil.showErrorMessage( this, e.toString() );
2227 e.printStackTrace();
2230 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
2231 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
2233 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
2235 catch ( final URISyntaxException e ) {
2236 AptxUtil.showErrorMessage( this, e.toString() );
2238 e.printStackTrace();
2241 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
2243 uri_str = "http://www.eol.org/search?q="
2244 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
2246 catch ( final UnsupportedEncodingException e ) {
2247 AptxUtil.showErrorMessage( this, e.toString() );
2248 e.printStackTrace();
2251 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
2253 uri_str = "http://www.uniprot.org/taxonomy/?query="
2254 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
2256 catch ( final UnsupportedEncodingException e ) {
2257 AptxUtil.showErrorMessage( this, e.toString() );
2258 e.printStackTrace();
2261 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
2263 uri_str = "http://www.eol.org/search?q="
2264 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
2266 catch ( final UnsupportedEncodingException e ) {
2267 AptxUtil.showErrorMessage( this, e.toString() );
2268 e.printStackTrace();
2271 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2273 JApplet applet = null;
2275 applet = obtainApplet();
2277 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
2279 catch ( final IOException e ) {
2280 AptxUtil.showErrorMessage( this, e.toString() );
2281 e.printStackTrace();
2283 catch ( final URISyntaxException e ) {
2284 AptxUtil.showErrorMessage( this, e.toString() );
2285 e.printStackTrace();
2289 cannotOpenBrowserWarningMessage( "taxonomic" );
2293 final void paintBranchCircular( final PhylogenyNode p,
2294 final PhylogenyNode c,
2296 final boolean radial_labels,
2297 final boolean to_pdf,
2298 final boolean to_graphics_file ) {
2299 final double angle = _urt_nodeid_angle_map.get( c.getId() );
2300 final double root_x = _root.getXcoord();
2301 final double root_y = _root.getYcoord();
2302 final double dx = root_x - p.getXcoord();
2303 final double dy = root_y - p.getYcoord();
2304 final double parent_radius = Math.sqrt( dx * dx + dy * dy );
2305 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
2306 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
2307 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
2308 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
2309 final double r2 = 2.0 * parent_radius;
2310 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
2312 drawLine( c.getXcoord(),
2314 root_x + ( Math.cos( angle ) * parent_radius ),
2315 root_y + ( Math.sin( angle ) * parent_radius ),
2317 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c ) );
2318 if ( c.isExternal() ) {
2319 final boolean is_in_found_nodes = isInFoundNodes( c );
2320 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
2321 && ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor != 1 ) ) {
2324 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
2328 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
2329 final double angle = _urt_nodeid_angle_map.get( c.getId() );
2330 final double root_x = _root.getXSecondary();
2331 final double root_y = _root.getYSecondary();
2332 final double dx = root_x - p.getXSecondary();
2333 final double dy = root_y - p.getYSecondary();
2334 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
2335 final double parent_radius = Math.sqrt( dx * dx + dy * dy );
2336 g.setColor( getTreeColorSet().getOvColor() );
2337 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
2338 final double r2 = 2.0 * parent_radius;
2339 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
2341 drawLine( c.getXSecondary(),
2343 root_x + ( Math.cos( angle ) * parent_radius ),
2344 root_y + ( Math.sin( angle ) * parent_radius ),
2346 if ( isInFoundNodes( c ) ) {
2347 g.setColor( getTreeColorSet().getFoundColor() );
2348 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
2352 final private void paintBranchLength( final Graphics2D g,
2353 final PhylogenyNode node,
2354 final boolean to_pdf,
2355 final boolean to_graphics_file ) {
2356 g.setFont( getTreeFontSet().getSmallFont() );
2357 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2358 g.setColor( Color.BLACK );
2361 g.setColor( getTreeColorSet().getBranchLengthColor() );
2363 if ( !node.isRoot() ) {
2364 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2365 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2366 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2368 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2369 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2370 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2373 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2374 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2378 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
2379 - getTreeFontSet()._small_max_descent, g );
2383 final private void paintBranchLite( final Graphics2D g,
2388 final PhylogenyNode node ) {
2389 g.setColor( getTreeColorSet().getOvColor() );
2390 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
2391 drawLine( x1, y1, x2, y2, g );
2393 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
2394 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
2395 ( g ).draw( _quad_curve );
2397 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
2398 final float dx = x2 - x1;
2399 final float dy = y2 - y1;
2400 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
2401 + ( dy * 0.8f ), x2, y2 );
2402 ( g ).draw( _cubic_curve );
2405 final float x2a = x2;
2406 final float x1a = x1;
2407 // draw the vertical line
2408 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
2409 drawLine( x1, y1, x1, y2, g );
2411 // draw the horizontal line
2412 drawLine( x1a, y2, x2a, y2, g );
2417 * Paint a branch which consists of a vertical and a horizontal bar
2418 * @param is_ind_found_nodes
2420 final private void paintBranchRectangular( final Graphics2D g,
2425 final PhylogenyNode node,
2426 final boolean to_pdf,
2427 final boolean to_graphics_file ) {
2428 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
2429 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
2430 drawLine( x1, y1, x2, y2, g );
2432 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
2433 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
2434 g.draw( _quad_curve );
2436 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
2437 final float dx = x2 - x1;
2438 final float dy = y2 - y1;
2439 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
2440 + ( dy * 0.8f ), x2, y2 );
2441 g.draw( _cubic_curve );
2444 final float x2a = x2;
2445 final float x1a = x1;
2447 if ( node.isFirstChildNode() || node.isLastChildNode()
2448 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
2449 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2450 if ( !to_graphics_file
2452 && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
2453 .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
2457 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2458 float x2c = x1 + EURO_D;
2462 drawLine( x1, y1, x2c, y2, g );
2464 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2466 y2_r = y2 - ROUNDED_D;
2470 drawLine( x1, y1, x1, y2_r, g );
2473 y2_r = y2 + ROUNDED_D;
2477 drawLine( x1, y1, x1, y2_r, g );
2481 drawLine( x1, y1, x1, y2, g );
2485 // draw the horizontal line
2486 if ( !to_graphics_file && !to_pdf
2487 && ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) {
2491 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
2492 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2493 x1_r = x1a + ROUNDED_D;
2495 drawLine( x1_r, y2, x2a, y2, g );
2498 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2499 final float x1c = x1a + EURO_D;
2501 drawLine( x1c, y2, x2a, y2, g );
2505 drawLine( x1a, y2, x2a, y2, g );
2509 final double w = PhylogenyMethods.getBranchWidthValue( node );
2510 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2511 x1_r = x1a + ROUNDED_D;
2513 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
2516 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2517 final float x1c = x1a + EURO_D;
2519 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
2523 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
2526 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2531 final double diff = y2 - y2_r;
2532 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
2535 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
2540 if ( node.isExternal() ) {
2541 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
2545 final void paintCircular( final Phylogeny phy,
2546 final double starting_angle,
2551 final boolean to_pdf,
2552 final boolean to_graphics_file ) {
2553 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
2554 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
2555 _root = phy.getRoot();
2556 _root.setXcoord( center_x );
2557 _root.setYcoord( center_y );
2558 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
2559 double current_angle = starting_angle;
2561 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2562 final PhylogenyNode n = it.next();
2563 if ( !n.isCollapse() ) {
2564 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
2565 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
2566 _urt_nodeid_angle_map.put( n.getId(), current_angle );
2567 _urt_nodeid_index_map.put( n.getId(), i++ );
2568 current_angle += ( TWO_PI / circ_num_ext_nodes );
2572 System.out.println( "is collapse" + n.getName() );
2575 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
2576 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
2579 void updateSetOfCollapsedExternalNodes() {
2580 final Phylogeny phy = getPhylogeny();
2581 _collapsed_external_nodeid_set.clear();
2582 if ( phy != null ) {
2583 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2584 final PhylogenyNode ext_node = it.next();
2585 PhylogenyNode n = ext_node;
2586 while ( !n.isRoot() ) {
2587 if ( n.isCollapse() ) {
2588 _collapsed_external_nodeid_set.add( ext_node.getId() );
2589 ext_node.setCollapse( true );
2598 final void paintCircularLite( final Phylogeny phy,
2599 final double starting_angle,
2603 final Graphics2D g ) {
2604 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
2605 _root = phy.getRoot();
2606 _root.setXSecondary( center_x );
2607 _root.setYSecondary( center_y );
2608 double current_angle = starting_angle;
2609 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2610 final PhylogenyNode n = it.next();
2611 n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) );
2612 n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) );
2613 _urt_nodeid_angle_map.put( n.getId(), current_angle );
2614 current_angle += ( TWO_PI / circ_num_ext_nodes );
2616 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
2619 final private double paintCirculars( final PhylogenyNode n,
2620 final Phylogeny phy,
2621 final float center_x,
2622 final float center_y,
2623 final double radius,
2624 final boolean radial_labels,
2626 final boolean to_pdf,
2627 final boolean to_graphics_file ) {
2628 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
2629 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
2630 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
2632 return _urt_nodeid_angle_map.get( n.getId() );
2635 final List<PhylogenyNode> descs = n.getDescendants();
2637 for( final PhylogenyNode desc : descs ) {
2638 sum += paintCirculars( desc,
2649 if ( !n.isRoot() ) {
2650 r = 1 - ( ( ( double ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
2652 final double theta = sum / descs.size();
2653 n.setXcoord( ( float ) ( center_x + r * radius * Math.cos( theta ) ) );
2654 n.setYcoord( ( float ) ( center_y + r * radius * Math.sin( theta ) ) );
2655 _urt_nodeid_angle_map.put( n.getId(), theta );
2656 for( final PhylogenyNode desc : descs ) {
2657 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
2663 final private void paintCircularsLite( final PhylogenyNode n,
2664 final Phylogeny phy,
2668 final Graphics2D g ) {
2669 if ( n.isExternal() ) {
2673 final List<PhylogenyNode> descs = n.getDescendants();
2674 for( final PhylogenyNode desc : descs ) {
2675 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
2678 if ( !n.isRoot() ) {
2679 r = 1 - ( ( ( float ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
2681 final double theta = _urt_nodeid_angle_map.get( n.getId() );
2682 n.setXSecondary( ( float ) ( center_x + radius * r * Math.cos( theta ) ) );
2683 n.setYSecondary( ( float ) ( center_y + radius * r * Math.sin( theta ) ) );
2684 for( final PhylogenyNode desc : descs ) {
2685 paintBranchCircularLite( n, desc, g );
2690 final private void paintCollapsedNode( final Graphics2D g,
2691 final PhylogenyNode node,
2692 final boolean to_graphics_file,
2693 final boolean to_pdf,
2694 final boolean is_in_found_nodes ) {
2696 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2699 else if ( is_in_found_nodes ) {
2700 c = getTreeColorSet().getFoundColor();
2702 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
2703 c = getTaxonomyBasedColor( node );
2705 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
2706 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2707 c = PhylogenyMethods.getBranchColorValue( node );
2710 c = getTreeColorSet().getCollapseFillColor();
2712 double d = node.getAllExternalDescendants().size();
2714 d = ( 3 * _y_distance ) / 3;
2717 d = ( Math.log10( d ) * _y_distance ) / 2.5;
2719 final int box_size = getOptions().getDefaultNodeShapeSize();
2720 if ( d < box_size ) {
2724 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
2725 ForesterUtil.roundToInt( node.getYcoord() ) );
2726 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
2727 ForesterUtil.roundToInt( node.getYcoord() - d ) );
2728 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
2729 ForesterUtil.roundToInt( node.getYcoord() + d ) );
2730 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
2732 g.fillPolygon( _polygon );
2734 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
2735 g.setColor( getBackground() );
2736 g.fillPolygon( _polygon );
2738 g.drawPolygon( _polygon );
2740 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
2741 g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
2742 .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
2747 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
2751 final public void paintComponent( final Graphics g ) {
2752 // Dimension currentSize = getSize();
2753 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
2754 // call the 'java.awt.Component.createImage(...)' method to get an
2756 // offscreenImage = createImage( currentSize.width, currentSize.height );
2757 // offscreenGraphics = offscreenImage.getGraphics();
2758 // offscreenDimension = currentSize;
2760 // super.paintComponent( g ); //why?
2761 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
2762 final Graphics2D g2d = ( Graphics2D ) g;
2763 g2d.setRenderingHints( _rendering_hints );
2764 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
2765 //g.drawImage( offscreenImage, 0, 0, this );
2769 public void update( final Graphics g ) {
2773 final private void paintConfidenceValues( final Graphics2D g,
2774 final PhylogenyNode node,
2775 final boolean to_pdf,
2776 final boolean to_graphics_file ) {
2777 final List<Confidence> confidences = node.getBranchData().getConfidences();
2778 // if ( confidences.size() == 1 ) {
2779 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
2780 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
2783 // conf_str = FORMATTER_CONFIDENCE.format( value );
2785 // else if ( confidences.size() > 1 ) {
2786 boolean one_ok = false;
2787 boolean not_first = false;
2788 Collections.sort( confidences );
2789 final StringBuilder sb = new StringBuilder();
2790 String conf_str = "";
2791 for( final Confidence confidence : confidences ) {
2792 final double value = confidence.getValue();
2793 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
2794 if ( value >= getOptions().getMinConfidenceValue() ) {
2803 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
2804 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
2805 if ( getOptions().isShowConfidenceStddev() ) {
2806 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
2808 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
2810 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
2817 conf_str = sb.toString();
2820 if ( conf_str.length() > 0 ) {
2821 final double parent_x = node.getParent().getXcoord();
2822 double x = node.getXcoord();
2823 g.setFont( getTreeFontSet().getSmallFont() );
2824 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2827 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2830 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2831 g.setColor( Color.BLACK );
2834 g.setColor( getTreeColorSet().getConfidenceColor() );
2837 .drawString( conf_str,
2839 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
2840 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
2845 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
2846 final int box_size = getOptions().getDefaultNodeShapeSize();
2847 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
2848 g.setColor( getTreeColorSet().getFoundColor() );
2849 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
2852 final private void paintGainedAndLostCharacters( final Graphics2D g,
2853 final PhylogenyNode node,
2854 final String gained,
2855 final String lost ) {
2856 if ( node.getParent() != null ) {
2857 final double parent_x = node.getParent().getXcoord();
2858 final double x = node.getXcoord();
2859 g.setFont( getTreeFontSet().getLargeFont() );
2860 g.setColor( getTreeColorSet().getGainedCharactersColor() );
2861 if ( Constants.SPECIAL_CUSTOM ) {
2862 g.setColor( Color.BLUE );
2865 .drawString( gained,
2866 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
2867 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
2869 g.setColor( getTreeColorSet().getLostCharactersColor() );
2870 TreePanel.drawString( lost,
2871 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
2872 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
2878 * Draw a box at the indicated node.
2885 final private void paintNodeBox( final double x,
2887 final PhylogenyNode node,
2889 final boolean to_pdf,
2890 final boolean to_graphics_file,
2891 final boolean is_in_found_nodes ) {
2892 if ( node.isCollapse() ) {
2895 // if this node should be highlighted, do so
2896 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
2897 g.setColor( getTreeColorSet().getFoundColor() );
2898 drawOval( x - 8, y - 8, 16, 16, g );
2899 drawOval( x - 9, y - 8, 17, 17, g );
2900 drawOval( x - 9, y - 9, 18, 18, g );
2902 if ( is_in_found_nodes ) {
2903 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
2906 Color outline_color = null;
2907 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2908 outline_color = Color.BLACK;
2910 else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
2911 final Event event = node.getNodeData().getEvent();
2912 if ( event.isDuplication() ) {
2913 outline_color = getTreeColorSet().getDuplicationBoxColor();
2915 else if ( event.isSpeciation() ) {
2916 outline_color = getTreeColorSet().getSpecBoxColor();
2918 else if ( event.isSpeciationOrDuplication() ) {
2919 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
2922 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
2923 outline_color = getTaxonomyBasedColor( node );
2926 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
2927 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
2928 outline_color = getTreeColorSet().getBranchColorForPdf();
2931 final int box_size = getOptions().getDefaultNodeShapeSize();
2932 final int half_box_size = box_size / 2;
2933 if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
2934 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
2935 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
2936 drawOvalGradient( x - half_box_size,
2941 to_pdf ? Color.WHITE : outline_color,
2942 to_pdf ? outline_color : getBackground(),
2945 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
2946 Color background = getBackground();
2948 background = Color.WHITE;
2950 drawOvalGradient( x - half_box_size,
2959 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
2960 g.setColor( outline_color );
2961 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
2964 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
2965 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
2966 drawRectGradient( x - half_box_size,
2971 to_pdf ? Color.WHITE : outline_color,
2972 to_pdf ? outline_color : getBackground(),
2975 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
2976 Color background = getBackground();
2978 background = Color.WHITE;
2980 drawRectGradient( x - half_box_size,
2989 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
2990 g.setColor( outline_color );
2991 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
2998 final private void paintNodeData( final Graphics2D g,
2999 final PhylogenyNode node,
3000 final boolean to_graphics_file,
3001 final boolean to_pdf,
3002 final boolean is_in_found_nodes ) {
3003 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
3006 if ( getOptions().isShowBranchLengthValues()
3007 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3008 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3009 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
3010 paintBranchLength( g, node, to_pdf, to_graphics_file );
3012 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
3016 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
3017 if ( getControlPanel().isShowTaxonomyImages()
3018 && ( getImageMap() != null )
3019 && !getImageMap().isEmpty()
3020 && node.getNodeData().isHasTaxonomy()
3021 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
3022 .getUris().isEmpty() ) ) {
3023 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
3025 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3026 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
3027 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
3029 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3030 g.setColor( Color.BLACK );
3032 else if ( is_in_found_nodes ) {
3033 g.setColor( getTreeColorSet().getFoundColor() );
3035 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3036 g.setColor( getTaxonomyBasedColor( node ) );
3038 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3039 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3040 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3042 else if ( to_pdf ) {
3043 g.setColor( Color.BLACK );
3046 g.setColor( getTreeColorSet().getSequenceColor() );
3049 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3051 _sb.append( node.getAllExternalDescendants().size() );
3054 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3055 if ( _sb.length() > 0 ) {
3058 _sb.append( node.getName() );
3060 if ( node.getNodeData().isHasSequence() ) {
3061 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3062 if ( _sb.length() > 0 ) {
3065 _sb.append( node.getNodeData().getSequence().getSymbol() );
3067 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3068 if ( _sb.length() > 0 ) {
3071 _sb.append( node.getNodeData().getSequence().getName() );
3073 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3074 if ( _sb.length() > 0 ) {
3077 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3078 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3081 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3084 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
3085 if ( _sb.length() > 0 ) {
3088 _sb.append( propertiesToString( node ) );
3090 g.setFont( getTreeFontSet().getLargeFont() );
3091 if ( is_in_found_nodes ) {
3092 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3094 double down_shift_factor = 3.0;
3095 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
3096 down_shift_factor = 1;
3098 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
3099 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
3100 final String sb_str = _sb.toString();
3101 // GUILHEM_BEG ______________
3102 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
3103 && ( _query_sequence != null ) ) {
3104 int nodeTextBoundsWidth = 0;
3105 if ( sb_str.length() > 0 ) {
3106 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
3107 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
3109 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
3110 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
3111 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
3112 g.setColor( getTreeColorSet().getBackgroundColor() );
3116 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
3117 for( final SequenceRelation seqRelation : seqRelations ) {
3118 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
3119 .getRef1().isEqual( _query_sequence ) )
3120 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
3121 .getSelectedItem() );
3122 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
3123 final double linePosX = node.getXcoord() + 2 + half_box_size;
3124 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
3125 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
3127 if ( sConfidence != null ) {
3128 double confidenceX = pos_x;
3129 if ( sb_str.length() > 0 ) {
3130 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
3131 + CONFIDENCE_LEFT_MARGIN;
3133 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
3134 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
3135 .getBounds().getWidth();
3136 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
3137 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
3140 if ( x + nodeTextBoundsWidth > 0 ) /* we only underline if there is something displayed */
3142 if ( nodeTextBoundsWidth == 0 ) {
3143 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
3146 nodeTextBoundsWidth += 2;
3148 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
3149 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
3156 if ( sb_str.length() > 0 ) {
3157 TreePanel.drawString( sb_str, pos_x, pos_y, g );
3159 // GUILHEM_END _____________
3160 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
3161 // TODO FIXME need to check this one!
3162 //if ( _sb.length() > 0 ) {
3163 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
3164 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
3166 // COMMENTED_OUT_BY_GUILHEM_END ________________
3167 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
3168 && ( node.getNodeData().getSequence().getAnnotations() != null )
3169 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
3170 if ( _sb.length() > 0 ) {
3171 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
3173 final Annotation ann = node.getNodeData().getSequence().getAnnotation( 0 );
3174 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3175 g.setColor( Color.BLACK );
3178 g.setColor( calculateColorForAnnotation( ann ) );
3180 final String ann_str = ann.asSimpleText().toString();
3181 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
3182 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
3184 _sb.append( ann_str );
3186 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3187 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3188 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3189 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
3190 && node.getNodeData().isHasBinaryCharacters() ) {
3191 if ( _sb.length() > 0 ) {
3192 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
3194 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3195 g.setColor( Color.BLACK );
3198 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
3200 if ( getControlPanel().isShowBinaryCharacters() ) {
3201 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
3202 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
3203 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
3204 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
3205 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
3206 .getLostCharactersAsStringBuffer().toString() );
3209 if ( DRAW_MEAN_COUNTS && node.isInternal() ) {
3210 final List<PhylogenyNode> ec = node.getAllExternalDescendants();
3213 for( final PhylogenyNode phylogenyNode : ec ) {
3215 if ( phylogenyNode.getNodeData().getBinaryCharacters() != null ) {
3216 sum += phylogenyNode.getNodeData().getBinaryCharacters().getPresentCount();
3219 final double mean = ForesterUtil.round( sum / count, 1 );
3220 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " ["
3221 + mean + "]", node.getXcoord() + x + 4 + half_box_size, node.getYcoord()
3222 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
3225 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
3226 node.getXcoord() + x + 4 + half_box_size,
3228 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
3231 paintGainedAndLostCharacters( g, node, "+"
3232 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
3233 + node.getNodeData().getBinaryCharacters().getLostCount() );
3239 private StringBuffer propertiesToString( final PhylogenyNode node ) {
3240 final PropertiesMap properties = node.getNodeData().getProperties();
3241 final StringBuffer sb = new StringBuffer();
3242 boolean first = true;
3243 for( final String ref : properties.getPropertyRefs() ) {
3250 final Property p = properties.getProperty( ref );
3251 sb.append( getPartAfterColon( p.getRef() ) );
3253 sb.append( p.getValue() );
3254 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
3255 sb.append( getPartAfterColon( p.getUnit() ) );
3261 final private static String getPartAfterColon( final String s ) {
3262 final int i = s.indexOf( ':' );
3263 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
3266 return s.substring( i + 1, s.length() );
3269 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
3270 final List<Uri> us = new ArrayList<Uri>();
3271 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
3272 for( final Uri uri : t.getUris() ) {
3277 for( final Uri uri : us ) {
3278 if ( uri != null ) {
3279 final String uri_str = uri.getValue().toString().toLowerCase();
3280 if ( getImageMap().containsKey( uri_str ) ) {
3281 final BufferedImage bi = getImageMap().get( uri_str );
3282 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
3283 double scaling_factor = 1;
3284 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
3285 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
3286 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
3288 // y = y - ( 0.9 * getYdistance() );
3289 final double hs = bi.getHeight() * scaling_factor;
3290 double ws = bi.getWidth() * scaling_factor + offset;
3291 final double my_y = y - ( 0.5 * hs );
3292 final int x_w = ( int ) ( x + ws + 0.5 );
3293 final int y_h = ( int ) ( my_y + hs + 0.5 );
3294 if ( ( x_w - x > 7 ) && ( y_h - my_y > 7 ) ) {
3296 ( int ) ( x + 0.5 + offset ),
3297 ( int ) ( my_y + 0.5 ),
3318 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
3319 final PhylogenyNode node,
3320 final boolean to_pdf,
3321 final boolean to_graphics_file,
3322 final boolean radial_labels,
3323 final double ur_angle,
3324 final boolean is_in_found_nodes ) {
3325 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
3328 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3329 g.setColor( Color.BLACK );
3331 else if ( is_in_found_nodes ) {
3332 g.setColor( getTreeColorSet().getFoundColor() );
3334 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3335 g.setColor( getTaxonomyBasedColor( node ) );
3338 g.setColor( getTreeColorSet().getSequenceColor() );
3342 if ( node.getNodeData().isHasTaxonomy()
3343 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3344 .isShowTaxonomyCommonNames() ) ) {
3345 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3346 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
3347 _sb.append( taxonomy.getTaxonomyCode() );
3350 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
3351 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
3352 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3353 _sb.append( taxonomy.getScientificName() );
3355 _sb.append( taxonomy.getCommonName() );
3358 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3359 _sb.append( taxonomy.getScientificName() );
3362 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3363 _sb.append( taxonomy.getCommonName() );
3367 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
3368 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3369 _sb.append( taxonomy.getScientificName() );
3373 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
3374 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3375 _sb.append( taxonomy.getCommonName() );
3380 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3382 _sb.append( node.getAllExternalDescendants().size() );
3385 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3386 if ( _sb.length() > 0 ) {
3389 _sb.append( node.getName() );
3391 if ( node.getNodeData().isHasSequence() ) {
3392 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3393 if ( _sb.length() > 0 ) {
3396 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3397 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3400 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3402 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3403 if ( _sb.length() > 0 ) {
3406 _sb.append( node.getNodeData().getSequence().getName() );
3409 g.setFont( getTreeFontSet().getLargeFont() );
3410 if ( is_in_found_nodes ) {
3411 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3413 if ( _sb.length() > 1 ) {
3414 final String sb_str = _sb.toString();
3416 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3417 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
3420 m = ( float ) ( ur_angle % TWO_PI );
3422 _at = g.getTransform();
3423 boolean need_to_reset = false;
3424 final float x_coord = node.getXcoord();
3425 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
3426 if ( radial_labels ) {
3427 need_to_reset = true;
3428 boolean left = false;
3429 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3433 g.rotate( m, x_coord, node.getYcoord() );
3435 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
3439 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3440 need_to_reset = true;
3441 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
3444 TreePanel.drawString( sb_str, x_coord, y_coord, g );
3445 if ( need_to_reset ) {
3446 g.setTransform( _at );
3451 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
3452 if ( node.isCollapse() ) {
3453 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
3454 paintCollapsedNode( g, node, false, false, false );
3458 if ( isInFoundNodes( node ) ) {
3459 g.setColor( getTreeColorSet().getFoundColor() );
3460 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
3463 if ( !node.isExternal() && !node.isCollapse() ) {
3464 boolean first_child = true;
3466 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3467 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3468 final PhylogenyNode child_node = node.getChildNode( i );
3470 if ( !isUniformBranchLengthsForCladogram() ) {
3471 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3474 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
3476 if ( first_child ) {
3477 first_child = false;
3478 y2 = node.getYSecondary()
3479 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
3480 .getNumberOfExternalNodes() ) );
3483 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3485 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
3486 new_x = x2 + node.getXSecondary();
3487 final float diff_y = node.getYSecondary() - y2;
3488 final float diff_x = node.getXSecondary() - new_x;
3489 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
3490 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
3492 child_node.setXSecondary( new_x );
3493 child_node.setYSecondary( y2 );
3494 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3499 final private void paintNodeRectangular( final Graphics2D g,
3500 final PhylogenyNode node,
3501 final boolean to_pdf,
3502 final boolean dynamically_hide,
3503 final int dynamic_hiding_factor,
3504 final boolean to_graphics_file ) {
3505 final boolean is_in_found_nodes = isInFoundNodes( node );
3506 if ( node.isCollapse() ) {
3507 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
3508 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3512 if ( node.isExternal() ) {
3513 ++_external_node_index;
3515 // Confidence values
3516 if ( getControlPanel().isShowConfidenceValues()
3517 && !node.isExternal()
3519 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
3520 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3521 && node.getBranchData().isHasConfidences() ) {
3522 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
3524 // Draw a line to root:
3525 if ( node.isRoot() && _phylogeny.isRooted() ) {
3526 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
3529 float new_x_min = Float.MAX_VALUE;
3530 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
3531 float min_dist = 1.5f;
3532 if ( !disallow_shortcutting ) {
3533 // System.out.println( dynamic_hiding_factor );
3534 if ( dynamic_hiding_factor > 4000 ) {
3537 else if ( dynamic_hiding_factor > 1000 ) {
3540 else if ( dynamic_hiding_factor > 100 ) {
3544 if ( !node.isExternal() && !node.isCollapse() ) {
3545 boolean first_child = true;
3547 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3548 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3549 final PhylogenyNode child_node = node.getChildNode( i );
3551 if ( !isUniformBranchLengthsForCladogram() ) {
3552 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3555 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
3557 if ( first_child ) {
3558 first_child = false;
3559 y2 = node.getYcoord()
3560 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
3563 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3565 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
3566 new_x = x2 + node.getXcoord();
3567 if ( dynamically_hide && ( x2 < new_x_min ) ) {
3570 final float diff_y = node.getYcoord() - y2;
3571 final float diff_x = node.getXcoord() - new_x;
3572 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
3573 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
3574 paintBranchRectangular( g,
3583 child_node.setXcoord( new_x );
3584 child_node.setYcoord( y2 );
3585 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3587 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
3589 if ( dynamically_hide
3590 && !is_in_found_nodes
3591 && ( ( node.isExternal() && ( _external_node_index % dynamic_hiding_factor != 1 ) ) || ( !node
3592 .isExternal() && ( ( new_x_min < 20 ) || ( _y_distance * node.getNumberOfExternalNodes() < getTreeFontSet()._fm_large
3593 .getHeight() ) ) ) ) ) {
3596 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3597 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
3600 final private void paintNodeWithRenderableData( final Graphics2D g,
3601 final PhylogenyNode node,
3602 final boolean to_graphics_file,
3603 final boolean to_pdf ) {
3604 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
3607 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
3610 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
3611 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
3612 RenderableDomainArchitecture rds = null;
3613 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
3615 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
3617 catch ( final ClassCastException cce ) {
3618 cce.printStackTrace();
3620 if ( rds != null ) {
3621 rds.setRenderingHeight( 6 );
3623 if ( getControlPanel().isShowTaxonomyCode()
3624 && ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( node ) ) ) ) {
3625 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
3627 if ( getControlPanel().isShowGeneNames()
3628 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
3629 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
3631 if ( getControlPanel().isShowGeneSymbols()
3632 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
3633 x += getTreeFontSet()._fm_large
3634 .stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
3636 if ( getControlPanel().isShowSequenceAcc()
3637 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3638 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
3642 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3643 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
3645 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
3650 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
3651 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
3652 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
3653 getStatisticsForExpressionValues(),
3654 getConfiguration() );
3657 PhylogenyNode my_node = node;
3658 if ( !getControlPanel().isDrawPhylogram() ) {
3659 my_node = getPhylogeny().getFirstExternalNode();
3661 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
3662 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
3664 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
3665 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
3667 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
3673 final private void paintOvRectangle( final Graphics2D g ) {
3674 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
3675 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
3676 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
3677 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
3678 final float width = getOvMaxWidth() / w_ratio;
3679 final float height = getOvMaxHeight() / h_ratio;
3680 final float x = getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / x_ratio;
3681 final float y = getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / y_ratio;
3682 g.setColor( getTreeColorSet().getFoundColor() );
3683 getOvRectangle().setRect( x, y, width, height );
3684 if ( ( width < 6 ) && ( height < 6 ) ) {
3685 drawRectFilled( x, y, 6, 6, g );
3686 getOvVirtualRectangle().setRect( x, y, 6, 6 );
3688 else if ( width < 6 ) {
3689 drawRectFilled( x, y, 6, height, g );
3690 getOvVirtualRectangle().setRect( x, y, 6, height );
3692 else if ( height < 6 ) {
3693 drawRectFilled( x, y, width, 6, g );
3694 getOvVirtualRectangle().setRect( x, y, width, 6 );
3697 drawRect( x, y, width, height, g );
3698 if ( isInOvRect() ) {
3699 drawRect( x + 1, y + 1, width - 2, height - 2, g );
3701 getOvVirtualRectangle().setRect( x, y, width, height );
3705 final void paintPhylogeny( final Graphics2D g,
3706 final boolean to_pdf,
3707 final boolean to_graphics_file,
3708 final int graphics_file_width,
3709 final int graphics_file_height,
3710 final int graphics_file_x,
3711 final int graphics_file_y ) {
3712 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
3715 if ( _control_panel.isShowSequenceRelations() ) {
3716 _query_sequence = _control_panel.getSelectedQuerySequence();
3718 // Color the background
3720 final Rectangle r = getVisibleRect();
3721 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
3722 g.setColor( getTreeColorSet().getBackgroundColor() );
3723 if ( !to_graphics_file ) {
3727 if ( getOptions().isPrintBlackAndWhite() ) {
3728 g.setColor( Color.WHITE );
3730 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
3734 if ( !to_graphics_file ) {
3735 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
3736 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
3740 g.setPaint( new GradientPaint( graphics_file_x,
3742 getTreeColorSet().getBackgroundColor(),
3744 graphics_file_y + graphics_file_height,
3745 getTreeColorSet().getBackgroundColorGradientBottom() ) );
3746 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
3749 g.setStroke( new BasicStroke( 1 ) );
3752 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
3754 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3755 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3756 _external_node_index = 0;
3757 // Position starting X of tree
3758 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
3759 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
3761 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
3762 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
3763 .getDistanceToParent() * getXcorrectionFactor() ) ) );
3766 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
3768 // Position starting Y of tree
3769 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
3770 + ( TreePanel.MOVE / 2.0f ) );
3771 final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
3772 if ( getControlPanel().isDynamicallyHideData() ) {
3773 if ( dynamic_hiding_factor > 1 ) {
3774 getControlPanel().setDynamicHidingIsOn( true );
3777 getControlPanel().setDynamicHidingIsOn( false );
3780 if ( _nodes_in_preorder == null ) {
3781 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
3783 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3784 _nodes_in_preorder[ i++ ] = it.next();
3787 //final PhylogenyNodeIterator it;
3788 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3789 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
3790 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
3792 for( int i = 0; i < _nodes_in_preorder.length; ++i ) {
3793 paintNodeRectangular( g, _nodes_in_preorder[ i ], to_pdf, getControlPanel().isDynamicallyHideData()
3794 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
3796 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
3797 if ( !( to_graphics_file || to_pdf ) ) {
3800 getVisibleRect().y + getVisibleRect().height,
3805 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
3808 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3809 paintPhylogenyLite( g );
3812 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
3813 if ( getControlPanel().getDynamicallyHideData() != null ) {
3814 getControlPanel().setDynamicHidingIsOn( false );
3816 final double angle = getStartingAngle();
3817 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
3818 _dynamic_hiding_factor = 0;
3819 if ( getControlPanel().isDynamicallyHideData() ) {
3820 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
3821 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
3823 if ( getControlPanel().getDynamicallyHideData() != null ) {
3824 if ( _dynamic_hiding_factor > 1 ) {
3825 getControlPanel().setDynamicHidingIsOn( true );
3828 getControlPanel().setDynamicHidingIsOn( false );
3831 paintUnrooted( _phylogeny.getRoot(),
3833 ( float ) ( angle + 2 * Math.PI ),
3838 if ( getOptions().isShowScale() ) {
3839 if ( !( to_graphics_file || to_pdf ) ) {
3842 getVisibleRect().y + getVisibleRect().height,
3847 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
3850 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3851 g.setColor( getTreeColorSet().getOvColor() );
3852 paintUnrootedLite( _phylogeny.getRoot(),
3854 angle + 2 * Math.PI,
3856 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
3857 paintOvRectangle( g );
3860 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3861 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
3862 final int d = radius + MOVE + getLongestExtNodeInfo();
3863 _dynamic_hiding_factor = 0;
3864 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
3865 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
3866 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
3868 if ( getControlPanel().getDynamicallyHideData() != null ) {
3869 if ( _dynamic_hiding_factor > 1 ) {
3870 getControlPanel().setDynamicHidingIsOn( true );
3873 getControlPanel().setDynamicHidingIsOn( false );
3876 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
3877 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3878 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
3879 : getOvMaxWidth() / 2 );
3880 double x_scale = 1.0;
3881 double y_scale = 1.0;
3882 int x_pos = getVisibleRect().x + getOvXPosition();
3883 int y_pos = getVisibleRect().y + getOvYPosition();
3884 if ( getWidth() > getHeight() ) {
3885 x_scale = ( double ) getHeight() / getWidth();
3886 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
3889 y_scale = ( double ) getWidth() / getHeight();
3890 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
3892 _at = g.getTransform();
3893 g.scale( x_scale, y_scale );
3894 paintCircularLite( _phylogeny,
3898 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
3901 g.setTransform( _at );
3902 paintOvRectangle( g );
3907 final private void paintPhylogenyLite( final Graphics2D g ) {
3908 //System.out.println( getVisibleRect().x + " " + getVisibleRect().y );
3911 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
3912 .getWidth() ) ) ) );
3913 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
3914 //final PhylogenyNodeIterator it;
3915 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3916 // paintNodeLite( g, it.next() );
3918 for( int i = 0; i < _nodes_in_preorder.length; ++i ) {
3919 paintNodeLite( g, _nodes_in_preorder[ i ] );
3921 paintOvRectangle( g );
3925 * Paint the root branch. (Differs from others because it will always be a
3926 * single horizontal line).
3927 * @param to_graphics_file
3929 * @return new x1 value
3931 final private void paintRootBranch( final Graphics2D g,
3934 final PhylogenyNode root,
3935 final boolean to_pdf,
3936 final boolean to_graphics_file ) {
3937 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
3938 float d = getXdistance();
3939 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
3940 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
3942 if ( d < MIN_ROOT_LENGTH ) {
3943 d = MIN_ROOT_LENGTH;
3945 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
3946 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
3949 final double w = PhylogenyMethods.getBranchWidthValue( root );
3950 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
3952 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
3955 final private void paintScale( final Graphics2D g,
3958 final boolean to_pdf,
3959 final boolean to_graphics_file ) {
3961 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
3963 final int y2 = y1 - 8;
3964 final int y3 = y1 - 4;
3965 g.setFont( getTreeFontSet().getSmallFont() );
3966 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3967 g.setColor( Color.BLACK );
3970 g.setColor( getTreeColorSet().getBranchLengthColor() );
3972 drawLine( x1, y1, x1, y2, g );
3973 drawLine( x2, y1, x2, y2, g );
3974 drawLine( x1, y3, x2, y3, g );
3975 if ( getScaleLabel() != null ) {
3976 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
3980 final private int paintTaxonomy( final Graphics2D g,
3981 final PhylogenyNode node,
3982 final boolean is_in_found_nodes,
3983 final boolean to_pdf,
3984 final boolean to_graphics_file,
3985 final double x_shift ) {
3986 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3987 g.setFont( getTreeFontSet().getLargeItalicFont() );
3988 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3989 g.setColor( Color.BLACK );
3991 else if ( is_in_found_nodes ) {
3992 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
3993 g.setColor( getTreeColorSet().getFoundColor() );
3995 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3996 g.setColor( getTaxonomyBasedColor( node ) );
3998 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3999 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
4000 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
4002 else if ( to_pdf ) {
4003 g.setColor( Color.BLACK );
4006 g.setColor( getTreeColorSet().getTaxonomyColor() );
4008 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
4009 final double start_y = node.getYcoord()
4010 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
4012 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
4013 _sb.append( taxonomy.getTaxonomyCode() );
4016 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
4017 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
4018 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4019 if ( getOptions().isAbbreviateScientificTaxonNames()
4020 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4021 abbreviateScientificName( taxonomy.getScientificName() );
4024 _sb.append( taxonomy.getScientificName() );
4027 _sb.append( taxonomy.getCommonName() );
4030 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4031 if ( getOptions().isAbbreviateScientificTaxonNames()
4032 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4033 abbreviateScientificName( taxonomy.getScientificName() );
4036 _sb.append( taxonomy.getScientificName() );
4040 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4041 _sb.append( taxonomy.getCommonName() );
4045 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4046 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4047 if ( getOptions().isAbbreviateScientificTaxonNames()
4048 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4049 abbreviateScientificName( taxonomy.getScientificName() );
4052 _sb.append( taxonomy.getScientificName() );
4057 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4058 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4059 _sb.append( taxonomy.getCommonName() );
4063 final String label = _sb.toString();
4065 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4066 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4067 // invert font color and background color to show that this is the query sequence
4068 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4072 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4073 g.setColor( getTreeColorSet().getBackgroundColor() );
4076 TreePanel.drawString( label, start_x, start_y, g );
4077 if ( is_in_found_nodes ) {
4078 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4081 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4085 private void abbreviateScientificName( final String sn ) {
4086 final String[] a = sn.split( "\\s+" );
4087 _sb.append( a[ 0 ].substring( 0, 1 ) );
4088 _sb.append( a[ 1 ].substring( 0, 2 ) );
4089 if ( a.length > 2 ) {
4090 for( int i = 2; i < a.length; i++ ) {
4092 _sb.append( a[ i ] );
4097 final private void paintUnrooted( final PhylogenyNode n,
4098 final double low_angle,
4099 final double high_angle,
4100 final boolean radial_labels,
4102 final boolean to_pdf,
4103 final boolean to_graphics_file ) {
4105 n.setXcoord( getWidth() / 2 );
4106 n.setYcoord( getHeight() / 2 );
4108 if ( n.isExternal() ) {
4109 paintNodeDataUnrootedCirc( g,
4114 ( high_angle + low_angle ) / 2,
4115 isInFoundNodes( n ) );
4118 final float num_enclosed = n.getNumberOfExternalNodes();
4119 final float x = n.getXcoord();
4120 final float y = n.getYcoord();
4121 double current_angle = low_angle;
4122 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4123 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4124 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4125 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4126 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4127 final PhylogenyNode desc = n.getChildNode( i );
4128 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4129 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4130 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4131 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4134 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4137 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4140 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4141 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4143 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4144 if ( desc.getDistanceToParent() < 0 ) {
4148 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4152 length = getUrtFactor();
4154 final double mid_angle = current_angle + arc_size / 2;
4155 final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
4156 final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
4157 desc.setXcoord( new_x );
4158 desc.setYcoord( new_y );
4159 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4160 current_angle += arc_size;
4161 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4162 drawLine( x, y, new_x, new_y, g );
4163 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
4166 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4170 final private void paintUnrootedLite( final PhylogenyNode n,
4171 final double low_angle,
4172 final double high_angle,
4174 final float urt_ov_factor ) {
4176 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / 2 );
4177 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / 2 );
4178 n.setXSecondary( x_pos );
4179 n.setYSecondary( y_pos );
4181 if ( n.isExternal() ) {
4184 final float num_enclosed = n.getNumberOfExternalNodes();
4185 final float x = n.getXSecondary();
4186 final float y = n.getYSecondary();
4187 double current_angle = low_angle;
4188 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4189 final PhylogenyNode desc = n.getChildNode( i );
4190 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4191 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4193 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4194 if ( desc.getDistanceToParent() < 0 ) {
4198 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4202 length = urt_ov_factor;
4204 final double mid_angle = current_angle + arc_size / 2;
4205 final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
4206 final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
4207 desc.setXSecondary( new_x );
4208 desc.setYSecondary( new_y );
4209 if ( isInFoundNodes( desc ) ) {
4210 g.setColor( getTreeColorSet().getFoundColor() );
4211 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4212 g.setColor( getTreeColorSet().getOvColor() );
4214 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4215 current_angle += arc_size;
4216 drawLine( x, y, new_x, new_y, g );
4220 final private void pasteSubtree( final PhylogenyNode node ) {
4221 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4222 errorMessageNoCutCopyPasteInUnrootedDisplay();
4225 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4226 JOptionPane.showMessageDialog( this,
4227 "No tree in buffer (need to copy or cut a subtree first)",
4228 "Attempt to paste with empty buffer",
4229 JOptionPane.ERROR_MESSAGE );
4232 final String label = getASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4233 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4234 final int r = JOptionPane.showOptionDialog( this,
4235 "How to paste subtree" + label + "?",
4237 JOptionPane.CLOSED_OPTION,
4238 JOptionPane.QUESTION_MESSAGE,
4242 boolean paste_as_sibling = true;
4244 paste_as_sibling = false;
4246 else if ( r != 0 ) {
4249 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4250 buffer_phy.setAllNodesToNotCollapse();
4251 buffer_phy.preOrderReId();
4252 buffer_phy.setRooted( true );
4253 boolean need_to_show_whole = false;
4254 if ( paste_as_sibling ) {
4255 if ( node.isRoot() ) {
4256 JOptionPane.showMessageDialog( this,
4257 "Cannot paste sibling to root",
4258 "Attempt to paste sibling to root",
4259 JOptionPane.ERROR_MESSAGE );
4262 buffer_phy.addAsSibling( node );
4265 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4266 need_to_show_whole = true;
4267 _phylogeny = buffer_phy;
4270 buffer_phy.addAsChild( node );
4273 if ( getCopiedAndPastedNodes() == null ) {
4274 setCopiedAndPastedNodes( new HashSet<Integer>() );
4276 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4277 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
4278 for( final PhylogenyNode n : nodes ) {
4279 node_ids.add( n.getId() );
4281 node_ids.add( node.getId() );
4282 getCopiedAndPastedNodes().addAll( node_ids );
4283 setNodeInPreorderToNull();
4284 _phylogeny.externalNodesHaveChanged();
4285 _phylogeny.clearHashIdToNodeMap();
4286 _phylogeny.recalculateNumberOfExternalDescendants( true );
4287 resetNodeIdToDistToLeafMap();
4289 if ( need_to_show_whole ) {
4290 getControlPanel().showWhole();
4295 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
4296 throws PrinterException {
4297 if ( page_index > 0 ) {
4298 return ( NO_SUCH_PAGE );
4301 final Graphics2D g2d = ( Graphics2D ) g;
4302 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
4303 // Turn off double buffering !?
4304 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
4305 // Turn double buffering back on !?
4306 return ( PAGE_EXISTS );
4310 final void recalculateMaxDistanceToRoot() {
4311 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
4315 * Remove all edit-node frames
4317 final void removeAllEditNodeJFrames() {
4318 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
4319 if ( _node_frames[ i ] != null ) {
4320 _node_frames[ i ].dispose();
4321 _node_frames[ i ] = null;
4324 _node_frame_index = 0;
4328 * Remove a node-edit frame.
4330 final void removeEditNodeFrame( final int i ) {
4331 _node_frame_index--;
4332 _node_frames[ i ] = null;
4333 if ( i < _node_frame_index ) {
4334 for( int j = 0; j < _node_frame_index - 1; j++ ) {
4335 _node_frames[ j ] = _node_frames[ j + 1 ];
4337 _node_frames[ _node_frame_index ] = null;
4341 final void reRoot( final PhylogenyNode node ) {
4342 if ( !getPhylogeny().isRerootable() ) {
4343 JOptionPane.showMessageDialog( this,
4344 "This is not rerootable",
4346 JOptionPane.WARNING_MESSAGE );
4349 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4350 JOptionPane.showMessageDialog( this,
4351 "Cannot reroot in unrooted display type",
4352 "Attempt to reroot tree in unrooted display",
4353 JOptionPane.WARNING_MESSAGE );
4356 getPhylogeny().reRoot( node );
4357 getPhylogeny().recalculateNumberOfExternalDescendants( true );
4358 resetNodeIdToDistToLeafMap();
4359 setNodeInPreorderToNull();
4360 resetPreferredSize();
4361 getMainPanel().adjustJScrollPane();
4363 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4364 getControlPanel().showWhole();
4368 final void resetNodeIdToDistToLeafMap() {
4369 _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
4372 final void resetPreferredSize() {
4373 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
4379 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
4380 if ( getControlPanel().isDrawPhylogram() ) {
4382 + getLongestExtNodeInfo()
4384 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
4387 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4389 + getLongestExtNodeInfo()
4390 + ForesterUtil.roundToInt( getXdistance()
4391 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
4395 + getLongestExtNodeInfo()
4396 + ForesterUtil.roundToInt( getXdistance()
4397 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
4400 setPreferredSize( new Dimension( x, y ) );
4403 public final void setArrowCursor() {
4404 setCursor( ARROW_CURSOR );
4408 final void setControlPanel( final ControlPanel atv_control ) {
4409 _control_panel = atv_control;
4412 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4413 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4416 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4417 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4420 public final void setEdited( final boolean edited ) {
4424 final void setFoundNodes( final Set<Integer> found_nodes ) {
4425 _found_nodes = found_nodes;
4428 final private void setInOv( final boolean in_ov ) {
4432 final void setInOvRect( final boolean in_ov_rect ) {
4433 _in_ov_rect = in_ov_rect;
4436 final void setLargeFonts() {
4437 getTreeFontSet().largeFonts();
4440 final void setLastMouseDragPointX( final float x ) {
4441 _last_drag_point_x = x;
4444 final void setLastMouseDragPointY( final float y ) {
4445 _last_drag_point_y = y;
4448 final void setLongestExtNodeInfo( final int i ) {
4449 _longest_ext_node_info = i;
4452 final void setMediumFonts() {
4453 getTreeFontSet().mediumFonts();
4456 final private void setOvMaxHeight( final float ov_max_height ) {
4457 _ov_max_height = ov_max_height;
4460 final private void setOvMaxWidth( final float ov_max_width ) {
4461 _ov_max_width = ov_max_width;
4464 final void setOvOn( final boolean ov_on ) {
4468 final private void setOvXcorrectionFactor( final float f ) {
4469 _ov_x_correction_factor = f;
4472 final private void setOvXDistance( final float ov_x_distance ) {
4473 _ov_x_distance = ov_x_distance;
4476 final private void setOvXPosition( final int ov_x_position ) {
4477 _ov_x_position = ov_x_position;
4480 final private void setOvYDistance( final float ov_y_distance ) {
4481 _ov_y_distance = ov_y_distance;
4484 final private void setOvYPosition( final int ov_y_position ) {
4485 _ov_y_position = ov_y_position;
4488 final private void setOvYStart( final int ov_y_start ) {
4489 _ov_y_start = ov_y_start;
4493 * Set parameters for printing the displayed tree
4498 public final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
4499 // updateStyle(); not needed?
4500 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4502 if ( recalc_longest_ext_node_info ) {
4503 calculateLongestExtNodeInfo();
4505 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
4506 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
4507 if ( ext_nodes == 1 ) {
4508 ext_nodes = max_depth;
4509 if ( ext_nodes < 1 ) {
4516 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4517 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
4518 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
4521 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
4522 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
4524 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
4525 if ( xdist < 0.0 ) {
4528 if ( ov_xdist < 0.0 ) {
4531 if ( ydist < 0.0 ) {
4534 setXdistance( xdist );
4535 setYdistance( ydist );
4536 setOvXDistance( ov_xdist );
4537 final double height = _phylogeny.getHeight();
4539 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
4540 setXcorrectionFactor( corr > 0 ? corr : 0 );
4541 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
4542 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
4545 setXcorrectionFactor( 0 );
4546 setOvXcorrectionFactor( 0 );
4548 _circ_max_depth = max_depth;
4553 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
4554 _graphics_type = graphics_type;
4558 final private void setScaleDistance( final double scale_distance ) {
4559 _scale_distance = scale_distance;
4562 final private void setScaleLabel( final String scale_label ) {
4563 _scale_label = scale_label;
4566 final void setSmallFonts() {
4567 getTreeFontSet().smallFonts();
4570 final void setStartingAngle( final double starting_angle ) {
4571 _urt_starting_angle = starting_angle;
4574 final void setSuperTinyFonts() {
4575 getTreeFontSet().superTinyFonts();
4578 final void setTextAntialias() {
4579 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4580 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
4581 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
4584 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
4587 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
4588 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4589 && !getMainPanel().getOptions().isShowDefaultNodeShapes()
4590 && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
4591 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
4594 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
4597 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
4598 RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
4600 catch ( final Throwable e ) {
4601 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
4605 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
4606 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
4610 final void setTinyFonts() {
4611 getTreeFontSet().tinyFonts();
4615 * Set a phylogeny tree.
4618 * an instance of a Phylogeny
4620 public final void setTree( final Phylogeny t ) {
4621 setNodeInPreorderToNull();
4625 final void setNodeInPreorderToNull() {
4626 _nodes_in_preorder = null;
4629 final void setTreeFile( final File treefile ) {
4630 _treefile = treefile;
4633 final private void setUpUrtFactor() {
4634 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4635 : getVisibleRect().height;
4636 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4637 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4640 final int max_depth = _circ_max_depth;
4641 if ( max_depth > 0 ) {
4642 setUrtFactor( d / ( 2 * max_depth ) );
4645 setUrtFactor( d / 2 );
4648 setUrtFactorOv( getUrtFactor() );
4651 final private void setUrtFactor( final float urt_factor ) {
4652 _urt_factor = urt_factor;
4655 final private void setUrtFactorOv( final float urt_factor_ov ) {
4656 _urt_factor_ov = urt_factor_ov;
4659 public final void setWaitCursor() {
4660 setCursor( WAIT_CURSOR );
4664 final void setXcorrectionFactor( final float f ) {
4665 _x_correction_factor = f;
4668 final void setXdistance( final float x ) {
4672 final void setYdistance( final float y ) {
4676 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
4678 if ( ( node.getName().length() > 0 )
4679 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
4680 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
4681 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
4682 || node.getBranchData().isHasConfidences() ) {
4683 _popup_buffer.setLength( 0 );
4685 if ( node.getName().length() > 0 ) {
4687 _popup_buffer.append( node.getName() );
4689 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
4691 boolean enc_data = false;
4692 final Taxonomy tax = node.getNodeData().getTaxonomy();
4693 if ( _popup_buffer.length() > 0 ) {
4694 _popup_buffer.append( "\n" );
4696 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
4697 _popup_buffer.append( "[" );
4698 _popup_buffer.append( tax.getTaxonomyCode() );
4699 _popup_buffer.append( "]" );
4702 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
4704 _popup_buffer.append( " " );
4706 _popup_buffer.append( tax.getScientificName() );
4709 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
4711 _popup_buffer.append( " (" );
4714 _popup_buffer.append( "(" );
4716 _popup_buffer.append( tax.getCommonName() );
4717 _popup_buffer.append( ")" );
4720 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
4722 _popup_buffer.append( " (" );
4725 _popup_buffer.append( "(" );
4727 _popup_buffer.append( tax.getAuthority() );
4728 _popup_buffer.append( ")" );
4731 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
4733 _popup_buffer.append( " [" );
4736 _popup_buffer.append( "[" );
4738 _popup_buffer.append( tax.getRank() );
4739 _popup_buffer.append( "]" );
4742 if ( tax.getSynonyms().size() > 0 ) {
4744 _popup_buffer.append( " " );
4746 _popup_buffer.append( "[" );
4748 for( final String syn : tax.getSynonyms() ) {
4749 if ( !ForesterUtil.isEmpty( syn ) ) {
4751 _popup_buffer.append( syn );
4752 if ( counter < tax.getSynonyms().size() ) {
4753 _popup_buffer.append( ", " );
4758 _popup_buffer.append( "]" );
4761 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
4762 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
4763 _popup_buffer.append( "[" );
4764 _popup_buffer.append( tax.getIdentifier().getProvider() );
4765 _popup_buffer.append( "] " );
4767 _popup_buffer.append( tax.getIdentifier().getValue() );
4771 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
4773 boolean enc_data = false;
4774 if ( _popup_buffer.length() > 0 ) {
4775 _popup_buffer.append( "\n" );
4777 final Sequence seq = node.getNodeData().getSequence();
4778 if ( seq.getAccession() != null ) {
4779 _popup_buffer.append( "[" );
4780 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
4781 _popup_buffer.append( seq.getAccession().getSource() );
4782 _popup_buffer.append( ":" );
4784 _popup_buffer.append( seq.getAccession().getValue() );
4785 _popup_buffer.append( "]" );
4788 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
4790 _popup_buffer.append( " [" );
4793 _popup_buffer.append( "[" );
4795 _popup_buffer.append( seq.getSymbol() );
4796 _popup_buffer.append( "]" );
4799 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
4801 _popup_buffer.append( " " );
4803 _popup_buffer.append( seq.getName() );
4806 if ( node.getNodeData().isHasDate() ) {
4808 if ( _popup_buffer.length() > 0 ) {
4809 _popup_buffer.append( "\n" );
4811 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
4813 if ( node.getNodeData().isHasDistribution() ) {
4815 if ( _popup_buffer.length() > 0 ) {
4816 _popup_buffer.append( "\n" );
4818 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
4820 if ( node.getBranchData().isHasConfidences() ) {
4821 final List<Confidence> confs = node.getBranchData().getConfidences();
4822 for( final Confidence confidence : confs ) {
4824 if ( _popup_buffer.length() > 0 ) {
4825 _popup_buffer.append( "\n" );
4827 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
4828 _popup_buffer.append( "[" );
4829 _popup_buffer.append( confidence.getType() );
4830 _popup_buffer.append( "] " );
4833 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
4835 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
4836 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4837 _popup_buffer.append( " (sd=" );
4838 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
4839 .getStandardDeviation(), getOptions()
4840 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
4841 _popup_buffer.append( ")" );
4845 if ( node.getNodeData().isHasProperties() ) {
4846 final PropertiesMap properties = node.getNodeData().getProperties();
4847 for( final String ref : properties.getPropertyRefs() ) {
4848 _popup_buffer.append( "\n" );
4849 final Property p = properties.getProperty( ref );
4850 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
4851 _popup_buffer.append( "=" );
4852 _popup_buffer.append( p.getValue() );
4853 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4854 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
4858 if ( _popup_buffer.length() > 0 ) {
4859 if ( !getConfiguration().isUseNativeUI() ) {
4861 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
4862 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
4863 if ( isInFoundNodes( node ) ) {
4864 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
4866 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4867 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
4870 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
4874 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
4876 _rollover_popup.setText( _popup_buffer.toString() );
4877 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
4879 e.getLocationOnScreen().x + 10,
4880 e.getLocationOnScreen().y
4882 _node_desc_popup.show();
4886 catch ( final Exception ex ) {
4891 final private void showNodeEditFrame( final PhylogenyNode n ) {
4892 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4893 // pop up edit box for single node
4894 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
4895 _node_frame_index++;
4898 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4902 final private void showNodeFrame( final PhylogenyNode n ) {
4903 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4904 // pop up edit box for single node
4905 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
4906 _node_frame_index++;
4909 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4913 final void subTree( final PhylogenyNode node ) {
4914 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4915 JOptionPane.showMessageDialog( this,
4916 "Cannot get a sub/super tree in unrooted display",
4917 "Attempt to get sub/super tree in unrooted display",
4918 JOptionPane.WARNING_MESSAGE );
4921 if ( node.isExternal() ) {
4922 JOptionPane.showMessageDialog( this,
4923 "Cannot get a subtree of a external node",
4924 "Attempt to get subtree of external node",
4925 JOptionPane.WARNING_MESSAGE );
4928 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
4929 JOptionPane.showMessageDialog( this,
4930 "Cannot get a subtree of the root node",
4931 "Attempt to get subtree of root node",
4932 JOptionPane.WARNING_MESSAGE );
4935 setNodeInPreorderToNull();
4936 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
4937 _sub_phylogenies[ _subtree_index ] = _phylogeny;
4938 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
4940 _phylogeny = subTree( node, _phylogeny );
4941 updateSubSuperTreeButton();
4943 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
4946 _main_panel.getControlPanel().showWhole();
4950 final boolean isCurrentTreeIsSubtree() {
4951 return ( _subtree_index > 0 );
4954 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
4955 final Phylogeny new_phy = new Phylogeny();
4956 new_phy.setRooted( true );
4957 new_phy.setName( source_phy.getName() );
4958 new_phy.setDescription( source_phy.getDescription() );
4959 new_phy.setType( source_phy.getType() );
4960 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
4961 new_phy.setConfidence( source_phy.getConfidence() );
4962 new_phy.setIdentifier( source_phy.getIdentifier() );
4963 new_phy.setRoot( new_root.copyNodeDataShallow() );
4965 for( final PhylogenyNode n : new_root.getDescendants() ) {
4966 new_phy.getRoot().setChildNode( i++, n );
4971 final void superTree() {
4972 setNodeInPreorderToNull();
4973 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
4974 for( final PhylogenyNode n : temp_root.getDescendants() ) {
4975 n.setParent( temp_root );
4977 _sub_phylogenies[ _subtree_index ] = null;
4978 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
4979 _phylogeny = _sub_phylogenies[ --_subtree_index ];
4980 updateSubSuperTreeButton();
4983 final void swap( final PhylogenyNode node ) {
4984 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
4987 if ( node.getNumberOfDescendants() > 2 ) {
4988 JOptionPane.showMessageDialog( this,
4989 "Cannot swap descendants of nodes with more than 2 descendants",
4990 "Cannot swap descendants",
4991 JOptionPane.ERROR_MESSAGE );
4994 if ( !node.isExternal() ) {
4995 node.swapChildren();
4996 setNodeInPreorderToNull();
4997 _phylogeny.externalNodesHaveChanged();
4998 _phylogeny.clearHashIdToNodeMap();
4999 _phylogeny.recalculateNumberOfExternalDescendants( true );
5000 resetNodeIdToDistToLeafMap();
5006 final void sortDescendants( final PhylogenyNode node ) {
5007 if ( !node.isExternal() ) {
5008 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
5009 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
5010 .isShowTaxonomyCommonNames() ) ) {
5011 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
5012 .isShowGeneSymbols() ) ) {
5013 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
5015 else if ( getControlPanel().isShowNodeNames() ) {
5016 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
5019 PhylogenyMethods.sortNodeDescendents( node, pri );
5020 setNodeInPreorderToNull();
5021 _phylogeny.externalNodesHaveChanged();
5022 _phylogeny.clearHashIdToNodeMap();
5023 _phylogeny.recalculateNumberOfExternalDescendants( true );
5024 resetNodeIdToDistToLeafMap();
5030 final private void switchDisplaygetPhylogenyGraphicsType() {
5031 switch ( getPhylogenyGraphicsType() ) {
5033 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5034 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5037 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5038 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5041 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5042 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5045 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5046 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5049 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5050 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5053 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5054 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5057 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5058 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5061 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5062 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5065 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5067 if ( getControlPanel().getDynamicallyHideData() != null ) {
5068 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5069 getControlPanel().getDynamicallyHideData().setEnabled( false );
5072 getControlPanel().getDynamicallyHideData().setEnabled( true );
5075 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5076 getControlPanel().setDrawPhylogramEnabled( true );
5079 getControlPanel().setDrawPhylogramEnabled( false );
5081 if ( getMainPanel().getMainFrame() == null ) {
5082 // Must be "E" applet version.
5083 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5084 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5087 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5091 final void taxColor() {
5092 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
5096 AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
5097 _control_panel.setColorBranches( true );
5098 if ( _control_panel.getColorBranchesCb() != null ) {
5099 _control_panel.getColorBranchesCb().setSelected( true );
5105 final void updateOvSettings() {
5106 switch ( getOptions().getOvPlacement() ) {
5108 setOvXPosition( OV_BORDER );
5109 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
5110 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
5113 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
5114 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
5115 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
5118 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
5119 setOvYPosition( OV_BORDER );
5120 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
5123 setOvXPosition( OV_BORDER );
5124 setOvYPosition( OV_BORDER );
5125 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
5130 final void updateOvSizes() {
5131 if ( ( getWidth() > 1.05 * getVisibleRect().width ) || ( getHeight() > 1.05 * getVisibleRect().height ) ) {
5133 float l = getLongestExtNodeInfo();
5134 final float w_ratio = getOvMaxWidth() / getWidth();
5136 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
5137 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
5139 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
5140 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
5143 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
5145 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
5146 if ( ov_xdist < 0.0 ) {
5149 if ( ydist < 0.0 ) {
5152 setOvXDistance( ov_xdist );
5153 final double height = _phylogeny.getHeight();
5155 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
5156 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
5159 setOvXcorrectionFactor( 0 );
5167 final void updateSubSuperTreeButton() {
5168 if ( _subtree_index < 1 ) {
5169 getControlPanel().deactivateButtonToReturnToSuperTree();
5172 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
5176 final void zoomInDomainStructure() {
5177 if ( _domain_structure_width < 2000 ) {
5178 _domain_structure_width *= 1.2;
5182 final void zoomOutDomainStructure() {
5183 if ( _domain_structure_width > 20 ) {
5184 _domain_structure_width *= 0.8;
5188 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5189 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5192 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5193 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5196 final private static boolean isSequenceEmpty( final Sequence seq ) {
5197 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5198 && ForesterUtil.isEmpty( seq.getSymbol() );
5201 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5202 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5203 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5204 .getSynonyms().isEmpty() );
5207 final private static boolean plusPressed( final int key_code ) {
5208 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5209 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5212 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
5213 _statistics_for_vector_data = statistics_for_expression_values;
5216 DescriptiveStatistics getStatisticsForExpressionValues() {
5217 return _statistics_for_vector_data;
5220 final private class SubtreeColorizationActionListener implements ActionListener {
5222 JColorChooser _chooser;
5223 PhylogenyNode _node;
5225 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5231 public void actionPerformed( final ActionEvent e ) {
5232 final Color c = _chooser.getColor();
5234 colorizeSubtree( c, _node );
5239 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
5240 getMainPanel().setImageMap( image_map );
5243 public synchronized Hashtable<String, BufferedImage> getImageMap() {
5244 return getMainPanel().getImageMap();