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 System.out.println( node.toString() );
1352 final void increaseDomainStructureEvalueThreshold() {
1353 if ( _domain_structure_e_value_thr_exp < 3 ) {
1354 _domain_structure_e_value_thr_exp += 1;
1358 final private void increaseOvSize() {
1359 if ( ( getOvMaxWidth() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 )
1360 && ( getOvMaxHeight() < getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
1361 .getHeight() / 2 ) ) {
1362 setOvMaxWidth( getOvMaxWidth() + 5 );
1363 setOvMaxHeight( getOvMaxHeight() + 5 );
1365 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1369 final void inferCommonPartOfScientificNames() {
1370 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1374 AptxUtil.inferCommonPartOfScientificNames( _phylogeny );
1379 final private void init() {
1380 _color_chooser = new JColorChooser();
1381 _rollover_popup = new JTextArea();
1382 _rollover_popup.setFont( POPUP_FONT );
1383 resetNodeIdToDistToLeafMap();
1385 setTreeFile( null );
1387 initializeOvSettings();
1388 setStartingAngle( TWO_PI * 3 / 4 );
1389 final ImageLoader il = new ImageLoader( this );
1390 new Thread( il ).start();
1393 final private void initializeOvSettings() {
1394 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
1395 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
1398 final void initNodeData() {
1399 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
1402 double max_original_domain_structure_width = 0.0;
1403 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1404 if ( node.getNodeData().isHasSequence()
1405 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1406 RenderableDomainArchitecture rds = null;
1407 if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
1408 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence().getDomainArchitecture(),
1409 getConfiguration() );
1410 node.getNodeData().getSequence().setDomainArchitecture( rds );
1413 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
1415 if ( getControlPanel().isShowDomainArchitectures() ) {
1416 final double dsw = rds.getOriginalSize().getWidth();
1417 if ( dsw > max_original_domain_structure_width ) {
1418 max_original_domain_structure_width = dsw;
1423 if ( getControlPanel().isShowDomainArchitectures() ) {
1424 final double ds_factor_width = _domain_structure_width / max_original_domain_structure_width;
1425 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
1426 if ( node.getNodeData().isHasSequence()
1427 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
1428 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
1429 .getSequence().getDomainArchitecture();
1430 rds.setRenderingFactorWidth( ds_factor_width );
1431 rds.setParameter( _domain_structure_e_value_thr_exp );
1437 final boolean inOv( final MouseEvent e ) {
1438 return ( ( e.getX() > getVisibleRect().x + getOvXPosition() + 1 )
1439 && ( e.getX() < getVisibleRect().x + getOvXPosition() + getOvMaxWidth() - 1 )
1440 && ( e.getY() > getVisibleRect().y + getOvYPosition() + 1 ) && ( e.getY() < getVisibleRect().y
1441 + getOvYPosition() + getOvMaxHeight() - 1 ) );
1444 final boolean inOvRectangle( final MouseEvent e ) {
1445 return ( ( e.getX() >= getOvRectangle().getX() - 1 )
1446 && ( e.getX() <= getOvRectangle().getX() + getOvRectangle().getWidth() + 1 )
1447 && ( e.getY() >= getOvRectangle().getY() - 1 ) && ( e.getY() <= getOvRectangle().getY()
1448 + getOvRectangle().getHeight() + 1 ) );
1451 final private boolean inOvVirtualRectangle( final int x, final int y ) {
1452 return ( ( x >= getOvVirtualRectangle().x - 1 )
1453 && ( x <= getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 )
1454 && ( y >= getOvVirtualRectangle().y - 1 ) && ( y <= getOvVirtualRectangle().y
1455 + getOvVirtualRectangle().height + 1 ) );
1458 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
1459 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
1462 final boolean isApplet() {
1463 return getMainPanel() instanceof MainPanelApplets;
1466 final private boolean isCanBlast( final PhylogenyNode node ) {
1467 return ( node.getNodeData().isHasSequence()
1468 && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil.isEmpty( node
1469 .getNodeData().getSequence().getAccession().getValue() ) )
1470 || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil
1471 .isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) && Blast
1472 .isContainsQueryForBlast( node ) );
1475 final boolean isCanCollapse() {
1476 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1479 final boolean isCanColorSubtree() {
1480 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
1483 final boolean isCanCopy() {
1484 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1487 final boolean isCanCut( final PhylogenyNode node ) {
1488 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node
1492 final boolean isCanDelete() {
1493 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
1496 final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
1497 if ( node.getNodeData().isHasSequence()
1498 && ( node.getNodeData().getSequence().getAccession() != null )
1499 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
1500 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
1501 && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
1502 .toLowerCase() ) ) {
1508 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
1509 if ( node.getNodeData().isHasTaxonomy()
1510 && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
1511 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
1512 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
1513 .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
1514 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
1515 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
1516 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
1517 .getNodeData().getTaxonomy().getIdentifier() != null )
1518 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
1519 .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
1527 final boolean isCanPaste() {
1528 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
1529 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
1532 final boolean isCanReroot() {
1533 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
1536 final boolean isCanSubtree( final PhylogenyNode node ) {
1537 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node
1538 .isRoot() || ( _subtree_index > 0 ) ) );
1541 final boolean isEdited() {
1545 final private boolean isInFoundNodes( final PhylogenyNode node ) {
1546 return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
1549 final private boolean isInOv() {
1553 final boolean isInOvRect() {
1557 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
1559 if ( getControlPanel().isShowTaxonomyImages() ) {
1560 y_dist = 40 + ( int ) getYdistance();
1562 return ( ( node.getYcoord() < getVisibleRect().getMinY() - y_dist )
1563 || ( node.getYcoord() > getVisibleRect().getMaxY() + y_dist ) || ( ( node.getParent() != null ) && ( node
1564 .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
1567 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
1568 return ( ( node.getYcoord() < getVisibleRect().getMinY() - 20 )
1569 || ( node.getYcoord() > getVisibleRect().getMaxY() + 20 )
1570 || ( node.getXcoord() < getVisibleRect().getMinX() - 20 ) || ( node.getXcoord() > getVisibleRect()
1571 .getMaxX() + 20 ) );
1574 final private boolean isNonLinedUpCladogram() {
1575 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
1578 final boolean isOvOn() {
1582 final boolean isPhyHasBranchLengths() {
1583 return _phy_has_branch_lengths;
1586 final private boolean isUniformBranchLengthsForCladogram() {
1587 return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP;
1590 final private void keyPressedCalls( final KeyEvent e ) {
1591 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
1592 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
1593 if ( !isInOvRect() ) {
1594 setInOvRect( true );
1597 else if ( isInOvRect() ) {
1598 setInOvRect( false );
1601 if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) {
1602 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1603 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
1604 getMainPanel().getTreeFontSet().mediumFonts();
1605 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1607 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1608 getMainPanel().getTreeFontSet().decreaseFontSize();
1609 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1611 else if ( plusPressed( e.getKeyCode() ) ) {
1612 getMainPanel().getTreeFontSet().increaseFontSize();
1613 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1617 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1618 || ( e.getKeyCode() == KeyEvent.VK_F ) ) {
1619 getControlPanel().showWhole();
1621 else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
1622 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
1623 if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) {
1624 if ( e.getKeyCode() == KeyEvent.VK_UP ) {
1625 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1626 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1628 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1629 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1630 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1632 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1633 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1634 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1635 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1637 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1638 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1639 Constants.WHEEL_ZOOM_IN_FACTOR );
1640 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1647 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1650 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1654 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1658 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1659 scroll_position.x = scroll_position.x + dx;
1660 scroll_position.y = scroll_position.y + dy;
1661 if ( scroll_position.x <= 0 ) {
1662 scroll_position.x = 0;
1665 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1666 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1667 if ( scroll_position.x >= max_x ) {
1668 scroll_position.x = max_x;
1671 if ( scroll_position.y <= 0 ) {
1672 scroll_position.y = 0;
1675 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1676 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1677 if ( scroll_position.y >= max_y ) {
1678 scroll_position.y = max_y;
1682 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1685 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1686 getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
1687 getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
1688 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1689 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1691 else if ( plusPressed( e.getKeyCode() ) ) {
1692 getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
1693 Constants.WHEEL_ZOOM_IN_FACTOR );
1694 getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
1695 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1697 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
1698 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1699 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1700 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
1701 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1704 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
1705 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1706 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1707 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
1708 if ( getStartingAngle() < 0 ) {
1709 setStartingAngle( TWO_PI + getStartingAngle() );
1711 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1714 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
1715 boolean selected = false;
1716 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
1717 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1721 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1723 if ( getMainPanel().getMainFrame() == null ) {
1724 // Must be "E" applet version.
1725 final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet();
1726 if ( ae.getlabelDirectionCbmi() != null ) {
1727 ae.getlabelDirectionCbmi().setSelected( selected );
1731 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
1735 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
1736 switchDisplaygetPhylogenyGraphicsType();
1739 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
1743 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
1744 MainFrame.cycleOverview( getOptions(), this );
1747 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
1750 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
1757 final private void makePopupMenus( final PhylogenyNode node ) {
1758 _node_popup_menu = new JPopupMenu();
1759 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
1760 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
1761 for( int i = 0; i < clickto_names.size(); i++ ) {
1762 final String title = clickto_names.get( i );
1763 _node_popup_menu_items[ i ] = new JMenuItem( title );
1764 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
1765 _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
1767 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
1768 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
1770 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
1771 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
1773 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
1774 if ( !getOptions().isEditable() ) {
1777 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
1779 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
1780 if ( !getOptions().isEditable() ) {
1783 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
1785 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
1786 if ( !getOptions().isEditable() ) {
1789 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
1791 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
1792 if ( !getOptions().isEditable() ) {
1795 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
1797 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
1798 if ( !getOptions().isEditable() ) {
1802 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
1803 if ( !getOptions().isEditable() ) {
1807 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
1808 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
1810 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
1811 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
1813 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
1814 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
1816 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
1817 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
1819 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
1820 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
1822 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
1823 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
1825 _node_popup_menu_items[ i ].addActionListener( this );
1826 _node_popup_menu.add( _node_popup_menu_items[ i ] );
1830 final void midpointRoot() {
1831 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
1834 if ( !_phylogeny.isRerootable() ) {
1835 JOptionPane.showMessageDialog( this,
1836 "This is not rerootable",
1838 JOptionPane.WARNING_MESSAGE );
1841 setNodeInPreorderToNull();
1843 PhylogenyMethods.midpointRoot( _phylogeny );
1844 resetNodeIdToDistToLeafMap();
1849 final void mouseClicked( final MouseEvent e ) {
1850 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
1851 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1852 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1853 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - getOvRectangle().getWidth() / 2.0 )
1855 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - getOvRectangle().getHeight() / 2.0 )
1863 final double max_x = getWidth() - getVisibleRect().width;
1864 final double max_y = getHeight() - getVisibleRect().height;
1871 getMainPanel().getCurrentScrollPane().getViewport()
1872 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
1873 setInOvRect( true );
1877 final PhylogenyNode node = findNode( e.getX(), e.getY() );
1878 if ( node != null ) {
1879 if ( !node.isRoot() && node.getParent().isCollapse() ) {
1882 _highlight_node = node;
1883 // Check if shift key is down
1884 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
1885 // Yes, so add to _found_nodes
1886 if ( getFoundNodes() == null ) {
1887 setFoundNodes( new HashSet<Integer>() );
1889 getFoundNodes().add( node.getId() );
1890 // Check if control key is down
1892 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
1893 // Yes, so pop-up menu
1894 displayNodePopupMenu( node, e.getX(), e.getY() );
1895 // Handle unadorned click
1898 // Check for right mouse button
1899 if ( e.getModifiers() == 4 ) {
1900 displayNodePopupMenu( node, e.getX(), e.getY() );
1903 // if not in _found_nodes, clear _found_nodes
1904 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
1909 // no node was clicked
1910 _highlight_node = null;
1916 final void mouseDragInBrowserPanel( final MouseEvent e ) {
1917 setCursor( MOVE_CURSOR );
1918 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1919 scroll_position.x -= ( e.getX() - getLastDragPointX() );
1920 scroll_position.y -= ( e.getY() - getLastDragPointY() );
1921 if ( scroll_position.x < 0 ) {
1922 scroll_position.x = 0;
1925 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1926 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1927 if ( scroll_position.x > max_x ) {
1928 scroll_position.x = max_x;
1931 if ( scroll_position.y < 0 ) {
1932 scroll_position.y = 0;
1935 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1936 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1937 if ( scroll_position.y > max_y ) {
1938 scroll_position.y = max_y;
1941 if ( isOvOn() || getOptions().isShowScale() ) {
1944 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1947 final void mouseDragInOvRectangle( final MouseEvent e ) {
1948 setCursor( HAND_CURSOR );
1949 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
1950 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
1951 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1952 double dx = ( w_ratio * e.getX() - w_ratio * getLastDragPointX() );
1953 double dy = ( h_ratio * e.getY() - h_ratio * getLastDragPointY() );
1954 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
1955 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
1956 if ( scroll_position.x <= 0 ) {
1957 scroll_position.x = 0;
1961 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1962 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1963 if ( scroll_position.x >= max_x ) {
1965 scroll_position.x = max_x;
1968 if ( scroll_position.y <= 0 ) {
1970 scroll_position.y = 0;
1973 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1974 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1975 if ( scroll_position.y >= max_y ) {
1977 scroll_position.y = max_y;
1981 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1982 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
1983 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
1986 final void mouseMoved( final MouseEvent e ) {
1987 requestFocusInWindow();
1988 if ( getControlPanel().isNodeDescPopup() ) {
1989 if ( _node_desc_popup != null ) {
1990 _node_desc_popup.hide();
1991 _node_desc_popup = null;
1994 if ( getOptions().isShowOverview() && isOvOn() ) {
1995 if ( inOvVirtualRectangle( e ) ) {
1996 if ( !isInOvRect() ) {
1997 setInOvRect( true );
2002 if ( isInOvRect() ) {
2003 setInOvRect( false );
2008 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
2017 final PhylogenyNode node = findNode( e.getX(), e.getY() );
2018 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
2019 // cursor is over a tree node
2020 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
2021 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
2022 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
2023 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
2024 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
2025 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
2026 setCursor( CUT_CURSOR );
2029 setCursor( HAND_CURSOR );
2030 if ( getControlPanel().isNodeDescPopup() ) {
2031 showNodeDataPopup( e, node );
2036 setCursor( ARROW_CURSOR );
2041 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
2042 setCursor( ARROW_CURSOR );
2045 final public void mouseWheelMoved( final MouseWheelEvent e ) {
2046 final int notches = e.getWheelRotation();
2047 if ( inOvVirtualRectangle( e ) ) {
2048 if ( !isInOvRect() ) {
2049 setInOvRect( true );
2054 if ( isInOvRect() ) {
2055 setInOvRect( false );
2059 if ( e.isControlDown() ) {
2060 if ( notches < 0 ) {
2061 getTreeFontSet().increaseFontSize();
2062 getControlPanel().displayedPhylogenyMightHaveChanged( true );
2065 getTreeFontSet().decreaseFontSize();
2066 getControlPanel().displayedPhylogenyMightHaveChanged( true );
2069 else if ( e.isShiftDown() ) {
2070 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
2071 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
2072 if ( notches < 0 ) {
2073 for( int i = 0; i < ( -notches ); ++i ) {
2074 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
2075 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2079 for( int i = 0; i < notches; ++i ) {
2080 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
2081 if ( getStartingAngle() < 0 ) {
2082 setStartingAngle( TWO_PI + getStartingAngle() );
2084 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2089 if ( notches < 0 ) {
2090 for( int i = 0; i < ( -notches ); ++i ) {
2091 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
2092 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2096 for( int i = 0; i < notches; ++i ) {
2097 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
2098 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2104 if ( notches < 0 ) {
2105 for( int i = 0; i < ( -notches ); ++i ) {
2106 getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR,
2107 Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
2108 getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR );
2109 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2113 for( int i = 0; i < notches; ++i ) {
2114 getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR );
2115 getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR,
2116 Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
2117 getControlPanel().displayedPhylogenyMightHaveChanged( false );
2122 requestFocusInWindow();
2126 final void multiplyUrtFactor( final float f ) {
2130 final JApplet obtainApplet() {
2131 return ( ( MainPanelApplets ) getMainPanel() ).getApplet();
2134 final private void openSeqWeb( final PhylogenyNode node ) {
2135 if ( !isCanOpenSeqWeb( node ) ) {
2136 cannotOpenBrowserWarningMessage( "sequence" );
2139 String uri_str = null;
2140 final Sequence seq = node.getNodeData().getSequence();
2141 final String source = seq.getAccession().getSource().toLowerCase();
2143 if ( source.toLowerCase().equals( "ncbi" ) ) {
2144 url = Constants.NCBI_ALL_DATABASE_SEARCH;
2147 final WebLink weblink = getConfiguration().getWebLink( source );
2148 url = weblink.getUrl().toString();
2151 uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
2153 catch ( final UnsupportedEncodingException e ) {
2154 AptxUtil.showErrorMessage( this, e.toString() );
2155 e.printStackTrace();
2157 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2159 JApplet applet = null;
2161 applet = obtainApplet();
2163 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
2165 catch ( final IOException e ) {
2166 AptxUtil.showErrorMessage( this, e.toString() );
2167 e.printStackTrace();
2169 catch ( final URISyntaxException e ) {
2170 AptxUtil.showErrorMessage( this, e.toString() );
2171 e.printStackTrace();
2175 cannotOpenBrowserWarningMessage( "sequence" );
2179 final private void openTaxWeb( final PhylogenyNode node ) {
2180 if ( !isCanOpenTaxWeb( node ) ) {
2181 cannotOpenBrowserWarningMessage( "taxonomic" );
2184 String uri_str = null;
2185 final Taxonomy tax = node.getNodeData().getTaxonomy();
2186 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
2187 && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
2188 final String type = tax.getIdentifier().getProvider().toLowerCase();
2189 final WebLink weblink = getConfiguration().getWebLink( type );
2191 uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
2193 catch ( final UnsupportedEncodingException e ) {
2194 AptxUtil.showErrorMessage( this, e.toString() );
2195 e.printStackTrace();
2198 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
2199 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
2201 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
2203 catch ( final URISyntaxException e ) {
2204 AptxUtil.showErrorMessage( this, e.toString() );
2206 e.printStackTrace();
2209 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
2211 uri_str = "http://www.eol.org/search?q="
2212 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
2214 catch ( final UnsupportedEncodingException e ) {
2215 AptxUtil.showErrorMessage( this, e.toString() );
2216 e.printStackTrace();
2219 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
2221 uri_str = "http://www.uniprot.org/taxonomy/?query="
2222 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
2224 catch ( final UnsupportedEncodingException e ) {
2225 AptxUtil.showErrorMessage( this, e.toString() );
2226 e.printStackTrace();
2229 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
2231 uri_str = "http://www.eol.org/search?q="
2232 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
2234 catch ( final UnsupportedEncodingException e ) {
2235 AptxUtil.showErrorMessage( this, e.toString() );
2236 e.printStackTrace();
2239 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2241 JApplet applet = null;
2243 applet = obtainApplet();
2245 AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
2247 catch ( final IOException e ) {
2248 AptxUtil.showErrorMessage( this, e.toString() );
2249 e.printStackTrace();
2251 catch ( final URISyntaxException e ) {
2252 AptxUtil.showErrorMessage( this, e.toString() );
2253 e.printStackTrace();
2257 cannotOpenBrowserWarningMessage( "taxonomic" );
2261 final void paintBranchCircular( final PhylogenyNode p,
2262 final PhylogenyNode c,
2264 final boolean radial_labels,
2265 final boolean to_pdf,
2266 final boolean to_graphics_file ) {
2267 final double angle = _urt_nodeid_angle_map.get( c.getId() );
2268 final double root_x = _root.getXcoord();
2269 final double root_y = _root.getYcoord();
2270 final double dx = root_x - p.getXcoord();
2271 final double dy = root_y - p.getYcoord();
2272 final double parent_radius = Math.sqrt( dx * dx + dy * dy );
2273 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
2274 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
2275 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
2276 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
2277 final double r2 = 2.0 * parent_radius;
2278 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
2280 drawLine( c.getXcoord(),
2282 root_x + ( Math.cos( angle ) * parent_radius ),
2283 root_y + ( Math.sin( angle ) * parent_radius ),
2285 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c ) );
2286 if ( c.isExternal() ) {
2287 final boolean is_in_found_nodes = isInFoundNodes( c );
2288 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
2289 && ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor != 1 ) ) {
2292 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
2296 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
2297 final double angle = _urt_nodeid_angle_map.get( c.getId() );
2298 final double root_x = _root.getXSecondary();
2299 final double root_y = _root.getYSecondary();
2300 final double dx = root_x - p.getXSecondary();
2301 final double dy = root_y - p.getYSecondary();
2302 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
2303 final double parent_radius = Math.sqrt( dx * dx + dy * dy );
2304 g.setColor( getTreeColorSet().getOvColor() );
2305 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
2306 final double r2 = 2.0 * parent_radius;
2307 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
2309 drawLine( c.getXSecondary(),
2311 root_x + ( Math.cos( angle ) * parent_radius ),
2312 root_y + ( Math.sin( angle ) * parent_radius ),
2314 if ( isInFoundNodes( c ) ) {
2315 g.setColor( getTreeColorSet().getFoundColor() );
2316 drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
2320 final private void paintBranchLength( final Graphics2D g,
2321 final PhylogenyNode node,
2322 final boolean to_pdf,
2323 final boolean to_graphics_file ) {
2324 g.setFont( getTreeFontSet().getSmallFont() );
2325 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2326 g.setColor( Color.BLACK );
2329 g.setColor( getTreeColorSet().getBranchLengthColor() );
2331 if ( !node.isRoot() ) {
2332 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2333 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2334 .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2336 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2337 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2338 .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2341 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
2342 .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
2346 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
2347 - getTreeFontSet()._small_max_descent, g );
2351 final private void paintBranchLite( final Graphics2D g,
2356 final PhylogenyNode node ) {
2357 g.setColor( getTreeColorSet().getOvColor() );
2358 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
2359 drawLine( x1, y1, x2, y2, g );
2361 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
2362 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
2363 ( g ).draw( _quad_curve );
2365 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
2366 final float dx = x2 - x1;
2367 final float dy = y2 - y1;
2368 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
2369 + ( dy * 0.8f ), x2, y2 );
2370 ( g ).draw( _cubic_curve );
2373 final float x2a = x2;
2374 final float x1a = x1;
2375 // draw the vertical line
2376 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
2377 drawLine( x1, y1, x1, y2, g );
2379 // draw the horizontal line
2380 drawLine( x1a, y2, x2a, y2, g );
2385 * Paint a branch which consists of a vertical and a horizontal bar
2386 * @param is_ind_found_nodes
2388 final private void paintBranchRectangular( final Graphics2D g,
2393 final PhylogenyNode node,
2394 final boolean to_pdf,
2395 final boolean to_graphics_file ) {
2396 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
2397 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
2398 drawLine( x1, y1, x2, y2, g );
2400 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
2401 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
2402 g.draw( _quad_curve );
2404 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
2405 final float dx = x2 - x1;
2406 final float dy = y2 - y1;
2407 _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
2408 + ( dy * 0.8f ), x2, y2 );
2409 g.draw( _cubic_curve );
2412 final float x2a = x2;
2413 final float x1a = x1;
2415 if ( node.isFirstChildNode() || node.isLastChildNode()
2416 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
2417 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2418 if ( !to_graphics_file
2420 && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
2421 .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
2425 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2426 float x2c = x1 + EURO_D;
2430 drawLine( x1, y1, x2c, y2, g );
2432 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2434 y2_r = y2 - ROUNDED_D;
2438 drawLine( x1, y1, x1, y2_r, g );
2441 y2_r = y2 + ROUNDED_D;
2445 drawLine( x1, y1, x1, y2_r, g );
2449 drawLine( x1, y1, x1, y2, g );
2453 // draw the horizontal line
2454 if ( !to_graphics_file && !to_pdf
2455 && ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) {
2459 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
2460 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2461 x1_r = x1a + ROUNDED_D;
2463 drawLine( x1_r, y2, x2a, y2, g );
2466 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2467 final float x1c = x1a + EURO_D;
2469 drawLine( x1c, y2, x2a, y2, g );
2473 drawLine( x1a, y2, x2a, y2, g );
2477 final double w = PhylogenyMethods.getBranchWidthValue( node );
2478 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2479 x1_r = x1a + ROUNDED_D;
2481 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
2484 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2485 final float x1c = x1a + EURO_D;
2487 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
2491 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
2494 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2499 final double diff = y2 - y2_r;
2500 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
2503 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
2508 if ( node.isExternal() ) {
2509 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
2513 final void paintCircular( final Phylogeny phy,
2514 final double starting_angle,
2519 final boolean to_pdf,
2520 final boolean to_graphics_file ) {
2521 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
2522 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
2523 _root = phy.getRoot();
2524 _root.setXcoord( center_x );
2525 _root.setYcoord( center_y );
2526 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
2527 double current_angle = starting_angle;
2529 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2530 final PhylogenyNode n = it.next();
2531 if ( !n.isCollapse() ) {
2532 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
2533 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
2534 _urt_nodeid_angle_map.put( n.getId(), current_angle );
2535 _urt_nodeid_index_map.put( n.getId(), i++ );
2536 current_angle += ( TWO_PI / circ_num_ext_nodes );
2540 System.out.println( "is collapse" + n.getName() );
2543 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
2544 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
2547 void updateSetOfCollapsedExternalNodes() {
2548 final Phylogeny phy = getPhylogeny();
2549 _collapsed_external_nodeid_set.clear();
2550 if ( phy != null ) {
2551 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2552 final PhylogenyNode ext_node = it.next();
2553 PhylogenyNode n = ext_node;
2554 while ( !n.isRoot() ) {
2555 if ( n.isCollapse() ) {
2556 _collapsed_external_nodeid_set.add( ext_node.getId() );
2557 ext_node.setCollapse( true );
2566 final void paintCircularLite( final Phylogeny phy,
2567 final double starting_angle,
2571 final Graphics2D g ) {
2572 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
2573 _root = phy.getRoot();
2574 _root.setXSecondary( center_x );
2575 _root.setYSecondary( center_y );
2576 double current_angle = starting_angle;
2577 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
2578 final PhylogenyNode n = it.next();
2579 n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) );
2580 n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) );
2581 _urt_nodeid_angle_map.put( n.getId(), current_angle );
2582 current_angle += ( TWO_PI / circ_num_ext_nodes );
2584 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
2587 final private double paintCirculars( final PhylogenyNode n,
2588 final Phylogeny phy,
2589 final float center_x,
2590 final float center_y,
2591 final double radius,
2592 final boolean radial_labels,
2594 final boolean to_pdf,
2595 final boolean to_graphics_file ) {
2596 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
2597 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
2598 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
2600 return _urt_nodeid_angle_map.get( n.getId() );
2603 final List<PhylogenyNode> descs = n.getDescendants();
2605 for( final PhylogenyNode desc : descs ) {
2606 sum += paintCirculars( desc,
2617 if ( !n.isRoot() ) {
2618 r = 1 - ( ( ( double ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
2620 final double theta = sum / descs.size();
2621 n.setXcoord( ( float ) ( center_x + r * radius * Math.cos( theta ) ) );
2622 n.setYcoord( ( float ) ( center_y + r * radius * Math.sin( theta ) ) );
2623 _urt_nodeid_angle_map.put( n.getId(), theta );
2624 for( final PhylogenyNode desc : descs ) {
2625 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
2631 final private void paintCircularsLite( final PhylogenyNode n,
2632 final Phylogeny phy,
2636 final Graphics2D g ) {
2637 if ( n.isExternal() ) {
2641 final List<PhylogenyNode> descs = n.getDescendants();
2642 for( final PhylogenyNode desc : descs ) {
2643 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
2646 if ( !n.isRoot() ) {
2647 r = 1 - ( ( ( float ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth );
2649 final double theta = _urt_nodeid_angle_map.get( n.getId() );
2650 n.setXSecondary( ( float ) ( center_x + radius * r * Math.cos( theta ) ) );
2651 n.setYSecondary( ( float ) ( center_y + radius * r * Math.sin( theta ) ) );
2652 for( final PhylogenyNode desc : descs ) {
2653 paintBranchCircularLite( n, desc, g );
2658 final private void paintCollapsedNode( final Graphics2D g,
2659 final PhylogenyNode node,
2660 final boolean to_graphics_file,
2661 final boolean to_pdf,
2662 final boolean is_in_found_nodes ) {
2664 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2667 else if ( is_in_found_nodes ) {
2668 c = getTreeColorSet().getFoundColor();
2670 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
2671 c = getTaxonomyBasedColor( node );
2673 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
2674 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2675 c = PhylogenyMethods.getBranchColorValue( node );
2678 c = getTreeColorSet().getCollapseFillColor();
2680 double d = node.getAllExternalDescendants().size();
2682 d = ( 3 * _y_distance ) / 3;
2685 d = ( Math.log10( d ) * _y_distance ) / 2.5;
2687 final int box_size = getOptions().getDefaultNodeShapeSize();
2688 if ( d < box_size ) {
2692 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
2693 ForesterUtil.roundToInt( node.getYcoord() ) );
2694 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
2695 ForesterUtil.roundToInt( node.getYcoord() - d ) );
2696 _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
2697 ForesterUtil.roundToInt( node.getYcoord() + d ) );
2698 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
2700 g.fillPolygon( _polygon );
2702 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
2703 g.setColor( getBackground() );
2704 g.fillPolygon( _polygon );
2706 g.drawPolygon( _polygon );
2708 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
2709 g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
2710 .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
2715 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
2719 final public void paintComponent( final Graphics g ) {
2720 // Dimension currentSize = getSize();
2721 // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) {
2722 // call the 'java.awt.Component.createImage(...)' method to get an
2724 // offscreenImage = createImage( currentSize.width, currentSize.height );
2725 // offscreenGraphics = offscreenImage.getGraphics();
2726 // offscreenDimension = currentSize;
2728 // super.paintComponent( g ); //why?
2729 //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics;
2730 final Graphics2D g2d = ( Graphics2D ) g;
2731 g2d.setRenderingHints( _rendering_hints );
2732 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
2733 //g.drawImage( offscreenImage, 0, 0, this );
2737 public void update( final Graphics g ) {
2741 final private void paintConfidenceValues( final Graphics2D g,
2742 final PhylogenyNode node,
2743 final boolean to_pdf,
2744 final boolean to_graphics_file ) {
2745 final List<Confidence> confidences = node.getBranchData().getConfidences();
2746 // if ( confidences.size() == 1 ) {
2747 // final double value = node.getBranchData().getConfidence( 0 ).getValue();
2748 // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
2751 // conf_str = FORMATTER_CONFIDENCE.format( value );
2753 // else if ( confidences.size() > 1 ) {
2754 boolean one_ok = false;
2755 boolean not_first = false;
2756 Collections.sort( confidences );
2757 final StringBuilder sb = new StringBuilder();
2758 String conf_str = "";
2759 for( final Confidence confidence : confidences ) {
2760 final double value = confidence.getValue();
2761 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
2762 if ( value >= getOptions().getMinConfidenceValue() ) {
2771 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
2772 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
2773 if ( getOptions().isShowConfidenceStddev() ) {
2774 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
2776 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
2778 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
2785 conf_str = sb.toString();
2788 if ( conf_str.length() > 0 ) {
2789 final double parent_x = node.getParent().getXcoord();
2790 double x = node.getXcoord();
2791 g.setFont( getTreeFontSet().getSmallFont() );
2792 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2795 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2798 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2799 g.setColor( Color.BLACK );
2802 g.setColor( getTreeColorSet().getConfidenceColor() );
2805 .drawString( conf_str,
2807 + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
2808 ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
2813 final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
2814 final int box_size = getOptions().getDefaultNodeShapeSize();
2815 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
2816 g.setColor( getTreeColorSet().getFoundColor() );
2817 g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
2820 final private void paintGainedAndLostCharacters( final Graphics2D g,
2821 final PhylogenyNode node,
2822 final String gained,
2823 final String lost ) {
2824 if ( node.getParent() != null ) {
2825 final double parent_x = node.getParent().getXcoord();
2826 final double x = node.getXcoord();
2827 g.setFont( getTreeFontSet().getLargeFont() );
2828 g.setColor( getTreeColorSet().getGainedCharactersColor() );
2829 if ( Constants.SPECIAL_CUSTOM ) {
2830 g.setColor( Color.BLUE );
2833 .drawString( gained,
2834 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
2835 ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
2837 g.setColor( getTreeColorSet().getLostCharactersColor() );
2838 TreePanel.drawString( lost,
2839 parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
2840 ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
2846 * Draw a box at the indicated node.
2853 final private void paintNodeBox( final double x,
2855 final PhylogenyNode node,
2857 final boolean to_pdf,
2858 final boolean to_graphics_file,
2859 final boolean is_in_found_nodes ) {
2860 if ( node.isCollapse() ) {
2863 // if this node should be highlighted, do so
2864 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
2865 g.setColor( getTreeColorSet().getFoundColor() );
2866 drawOval( x - 8, y - 8, 16, 16, g );
2867 drawOval( x - 9, y - 8, 17, 17, g );
2868 drawOval( x - 9, y - 9, 18, 18, g );
2870 if ( is_in_found_nodes ) {
2871 paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
2874 Color outline_color = null;
2875 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2876 outline_color = Color.BLACK;
2878 else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
2879 final Event event = node.getNodeData().getEvent();
2880 if ( event.isDuplication() ) {
2881 outline_color = getTreeColorSet().getDuplicationBoxColor();
2883 else if ( event.isSpeciation() ) {
2884 outline_color = getTreeColorSet().getSpecBoxColor();
2886 else if ( event.isSpeciationOrDuplication() ) {
2887 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
2890 else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
2891 outline_color = getTaxonomyBasedColor( node );
2894 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
2895 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
2896 outline_color = getTreeColorSet().getBranchColorForPdf();
2899 final int box_size = getOptions().getDefaultNodeShapeSize();
2900 final int half_box_size = box_size / 2;
2901 if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
2902 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
2903 if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
2904 drawOvalGradient( x - half_box_size,
2909 to_pdf ? Color.WHITE : outline_color,
2910 to_pdf ? outline_color : getBackground(),
2913 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
2914 Color background = getBackground();
2916 background = Color.WHITE;
2918 drawOvalGradient( x - half_box_size,
2927 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
2928 g.setColor( outline_color );
2929 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
2932 else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
2933 if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
2934 drawRectGradient( x - half_box_size,
2939 to_pdf ? Color.WHITE : outline_color,
2940 to_pdf ? outline_color : getBackground(),
2943 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
2944 Color background = getBackground();
2946 background = Color.WHITE;
2948 drawRectGradient( x - half_box_size,
2957 else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
2958 g.setColor( outline_color );
2959 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
2966 final private void paintNodeData( final Graphics2D g,
2967 final PhylogenyNode node,
2968 final boolean to_graphics_file,
2969 final boolean to_pdf,
2970 final boolean is_in_found_nodes ) {
2971 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
2974 if ( getOptions().isShowBranchLengthValues()
2975 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
2976 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
2977 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
2978 paintBranchLength( g, node, to_pdf, to_graphics_file );
2980 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
2984 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
2985 if ( getControlPanel().isShowTaxonomyImages()
2986 && ( getImageMap() != null )
2987 && !getImageMap().isEmpty()
2988 && node.getNodeData().isHasTaxonomy()
2989 && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
2990 .getUris().isEmpty() ) ) {
2991 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
2993 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
2994 .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
2995 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
2997 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2998 g.setColor( Color.BLACK );
3000 else if ( is_in_found_nodes ) {
3001 g.setColor( getTreeColorSet().getFoundColor() );
3003 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3004 g.setColor( getTaxonomyBasedColor( node ) );
3006 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3007 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3008 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3010 else if ( to_pdf ) {
3011 g.setColor( Color.BLACK );
3014 g.setColor( getTreeColorSet().getSequenceColor() );
3017 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3019 _sb.append( node.getAllExternalDescendants().size() );
3022 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3023 if ( _sb.length() > 0 ) {
3026 _sb.append( node.getName() );
3028 if ( node.getNodeData().isHasSequence() ) {
3029 if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
3030 if ( _sb.length() > 0 ) {
3033 _sb.append( node.getNodeData().getSequence().getSymbol() );
3035 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3036 if ( _sb.length() > 0 ) {
3039 _sb.append( node.getNodeData().getSequence().getName() );
3041 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3042 if ( _sb.length() > 0 ) {
3045 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3046 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3049 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3052 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
3053 if ( _sb.length() > 0 ) {
3056 _sb.append( propertiesToString( node ) );
3058 g.setFont( getTreeFontSet().getLargeFont() );
3059 if ( is_in_found_nodes ) {
3060 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3062 double down_shift_factor = 3.0;
3063 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
3064 down_shift_factor = 1;
3066 final double pos_x = node.getXcoord() + x + 2 + half_box_size;
3067 final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
3068 final String sb_str = _sb.toString();
3069 // GUILHEM_BEG ______________
3070 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
3071 && ( _query_sequence != null ) ) {
3072 int nodeTextBoundsWidth = 0;
3073 if ( sb_str.length() > 0 ) {
3074 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
3075 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
3077 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
3078 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
3079 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
3080 g.setColor( getTreeColorSet().getBackgroundColor() );
3084 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
3085 for( final SequenceRelation seqRelation : seqRelations ) {
3086 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
3087 .getRef1().isEqual( _query_sequence ) )
3088 && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
3089 .getSelectedItem() );
3090 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
3091 final double linePosX = node.getXcoord() + 2 + half_box_size;
3092 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
3093 .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
3095 if ( sConfidence != null ) {
3096 double confidenceX = pos_x;
3097 if ( sb_str.length() > 0 ) {
3098 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
3099 + CONFIDENCE_LEFT_MARGIN;
3101 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
3102 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
3103 .getBounds().getWidth();
3104 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
3105 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
3108 if ( x + nodeTextBoundsWidth > 0 ) /* we only underline if there is something displayed */
3110 if ( nodeTextBoundsWidth == 0 ) {
3111 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
3114 nodeTextBoundsWidth += 2;
3116 g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
3117 + nodeTextBoundsWidth, 3 + ( int ) pos_y );
3124 if ( sb_str.length() > 0 ) {
3125 TreePanel.drawString( sb_str, pos_x, pos_y, g );
3127 // GUILHEM_END _____________
3128 // COMMENTED_OUT_BY_GUILHEM_BEG _______________
3129 // TODO FIXME need to check this one!
3130 //if ( _sb.length() > 0 ) {
3131 // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
3132 // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
3134 // COMMENTED_OUT_BY_GUILHEM_END ________________
3135 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
3136 && ( node.getNodeData().getSequence().getAnnotations() != null )
3137 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
3138 if ( _sb.length() > 0 ) {
3139 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
3141 final Annotation ann = node.getNodeData().getSequence().getAnnotation( 0 );
3142 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3143 g.setColor( Color.BLACK );
3146 g.setColor( calculateColorForAnnotation( ann ) );
3148 final String ann_str = ann.asSimpleText().toString();
3149 TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
3150 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
3152 _sb.append( ann_str );
3154 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3155 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
3156 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
3157 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
3158 && node.getNodeData().isHasBinaryCharacters() ) {
3159 if ( _sb.length() > 0 ) {
3160 x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
3162 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3163 g.setColor( Color.BLACK );
3166 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
3168 if ( getControlPanel().isShowBinaryCharacters() ) {
3169 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
3170 .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
3171 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
3172 paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
3173 .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
3174 .getLostCharactersAsStringBuffer().toString() );
3177 if ( DRAW_MEAN_COUNTS && node.isInternal() ) {
3178 final List<PhylogenyNode> ec = node.getAllExternalDescendants();
3181 for( final PhylogenyNode phylogenyNode : ec ) {
3183 if ( phylogenyNode.getNodeData().getBinaryCharacters() != null ) {
3184 sum += phylogenyNode.getNodeData().getBinaryCharacters().getPresentCount();
3187 final double mean = ForesterUtil.round( sum / count, 1 );
3188 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " ["
3189 + mean + "]", node.getXcoord() + x + 4 + half_box_size, node.getYcoord()
3190 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
3193 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
3194 node.getXcoord() + x + 4 + half_box_size,
3196 + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
3199 paintGainedAndLostCharacters( g, node, "+"
3200 + node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
3201 + node.getNodeData().getBinaryCharacters().getLostCount() );
3207 private StringBuffer propertiesToString( final PhylogenyNode node ) {
3208 final PropertiesMap properties = node.getNodeData().getProperties();
3209 final StringBuffer sb = new StringBuffer();
3210 boolean first = true;
3211 for( final String ref : properties.getPropertyRefs() ) {
3218 final Property p = properties.getProperty( ref );
3219 sb.append( getPartAfterColon( p.getRef() ) );
3221 sb.append( p.getValue() );
3222 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
3223 sb.append( getPartAfterColon( p.getUnit() ) );
3229 final private static String getPartAfterColon( final String s ) {
3230 final int i = s.indexOf( ':' );
3231 if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
3234 return s.substring( i + 1, s.length() );
3237 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
3238 final List<Uri> us = new ArrayList<Uri>();
3239 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
3240 for( final Uri uri : t.getUris() ) {
3245 for( final Uri uri : us ) {
3246 if ( uri != null ) {
3247 final String uri_str = uri.getValue().toString().toLowerCase();
3248 if ( getImageMap().containsKey( uri_str ) ) {
3249 final BufferedImage bi = getImageMap().get( uri_str );
3250 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
3251 double scaling_factor = 1;
3252 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
3253 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
3254 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
3256 // y = y - ( 0.9 * getYdistance() );
3257 final double hs = bi.getHeight() * scaling_factor;
3258 double ws = bi.getWidth() * scaling_factor + offset;
3259 final double my_y = y - ( 0.5 * hs );
3260 final int x_w = ( int ) ( x + ws + 0.5 );
3261 final int y_h = ( int ) ( my_y + hs + 0.5 );
3262 if ( ( x_w - x > 7 ) && ( y_h - my_y > 7 ) ) {
3264 ( int ) ( x + 0.5 + offset ),
3265 ( int ) ( my_y + 0.5 ),
3286 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
3287 final PhylogenyNode node,
3288 final boolean to_pdf,
3289 final boolean to_graphics_file,
3290 final boolean radial_labels,
3291 final double ur_angle,
3292 final boolean is_in_found_nodes ) {
3293 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
3296 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3297 g.setColor( Color.BLACK );
3299 else if ( is_in_found_nodes ) {
3300 g.setColor( getTreeColorSet().getFoundColor() );
3302 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3303 g.setColor( getTaxonomyBasedColor( node ) );
3306 g.setColor( getTreeColorSet().getSequenceColor() );
3310 if ( node.getNodeData().isHasTaxonomy()
3311 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
3312 .isShowTaxonomyCommonNames() ) ) {
3313 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3314 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
3315 _sb.append( taxonomy.getTaxonomyCode() );
3318 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
3319 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
3320 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3321 _sb.append( taxonomy.getScientificName() );
3323 _sb.append( taxonomy.getCommonName() );
3326 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3327 _sb.append( taxonomy.getScientificName() );
3330 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3331 _sb.append( taxonomy.getCommonName() );
3335 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
3336 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3337 _sb.append( taxonomy.getScientificName() );
3341 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
3342 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3343 _sb.append( taxonomy.getCommonName() );
3348 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3350 _sb.append( node.getAllExternalDescendants().size() );
3353 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3354 if ( _sb.length() > 0 ) {
3357 _sb.append( node.getName() );
3359 if ( node.getNodeData().isHasSequence() ) {
3360 if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3361 if ( _sb.length() > 0 ) {
3364 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3365 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3368 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3370 if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3371 if ( _sb.length() > 0 ) {
3374 _sb.append( node.getNodeData().getSequence().getName() );
3377 g.setFont( getTreeFontSet().getLargeFont() );
3378 if ( is_in_found_nodes ) {
3379 g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3381 if ( _sb.length() > 1 ) {
3382 final String sb_str = _sb.toString();
3384 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3385 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
3388 m = ( float ) ( ur_angle % TWO_PI );
3390 _at = g.getTransform();
3391 boolean need_to_reset = false;
3392 final float x_coord = node.getXcoord();
3393 final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
3394 if ( radial_labels ) {
3395 need_to_reset = true;
3396 boolean left = false;
3397 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3401 g.rotate( m, x_coord, node.getYcoord() );
3403 g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
3407 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3408 need_to_reset = true;
3409 g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
3412 TreePanel.drawString( sb_str, x_coord, y_coord, g );
3413 if ( need_to_reset ) {
3414 g.setTransform( _at );
3419 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
3420 if ( node.isCollapse() ) {
3421 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
3422 paintCollapsedNode( g, node, false, false, false );
3426 if ( isInFoundNodes( node ) ) {
3427 g.setColor( getTreeColorSet().getFoundColor() );
3428 drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
3431 if ( !node.isExternal() && !node.isCollapse() ) {
3432 boolean first_child = true;
3434 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3435 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3436 final PhylogenyNode child_node = node.getChildNode( i );
3438 if ( !isUniformBranchLengthsForCladogram() ) {
3439 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3442 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
3444 if ( first_child ) {
3445 first_child = false;
3446 y2 = node.getYSecondary()
3447 - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node
3448 .getNumberOfExternalNodes() ) );
3451 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3453 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
3454 new_x = x2 + node.getXSecondary();
3455 final float diff_y = node.getYSecondary() - y2;
3456 final float diff_x = node.getXSecondary() - new_x;
3457 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
3458 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
3460 child_node.setXSecondary( new_x );
3461 child_node.setYSecondary( y2 );
3462 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3467 final private void paintNodeRectangular( final Graphics2D g,
3468 final PhylogenyNode node,
3469 final boolean to_pdf,
3470 final boolean dynamically_hide,
3471 final int dynamic_hiding_factor,
3472 final boolean to_graphics_file ) {
3473 final boolean is_in_found_nodes = isInFoundNodes( node );
3474 if ( node.isCollapse() ) {
3475 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
3476 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3480 if ( node.isExternal() ) {
3481 ++_external_node_index;
3483 // Confidence values
3484 if ( getControlPanel().isShowConfidenceValues()
3485 && !node.isExternal()
3487 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
3488 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3489 && node.getBranchData().isHasConfidences() ) {
3490 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
3492 // Draw a line to root:
3493 if ( node.isRoot() && _phylogeny.isRooted() ) {
3494 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
3497 float new_x_min = Float.MAX_VALUE;
3498 final boolean disallow_shortcutting = dynamic_hiding_factor < 40;
3499 float min_dist = 1.5f;
3500 if ( !disallow_shortcutting ) {
3501 // System.out.println( dynamic_hiding_factor );
3502 if ( dynamic_hiding_factor > 4000 ) {
3505 else if ( dynamic_hiding_factor > 1000 ) {
3508 else if ( dynamic_hiding_factor > 100 ) {
3512 if ( !node.isExternal() && !node.isCollapse() ) {
3513 boolean first_child = true;
3515 final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3516 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3517 final PhylogenyNode child_node = node.getChildNode( i );
3519 if ( !isUniformBranchLengthsForCladogram() ) {
3520 factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3523 factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node );
3525 if ( first_child ) {
3526 first_child = false;
3527 y2 = node.getYcoord()
3528 - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
3531 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3533 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
3534 new_x = x2 + node.getXcoord();
3535 if ( dynamically_hide && ( x2 < new_x_min ) ) {
3538 final float diff_y = node.getYcoord() - y2;
3539 final float diff_x = node.getXcoord() - new_x;
3540 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
3541 || ( diff_x < -min_dist ) || to_graphics_file || to_pdf ) {
3542 paintBranchRectangular( g,
3551 child_node.setXcoord( new_x );
3552 child_node.setYcoord( y2 );
3553 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3555 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
3557 if ( dynamically_hide
3558 && !is_in_found_nodes
3559 && ( ( node.isExternal() && ( _external_node_index % dynamic_hiding_factor != 1 ) ) || ( !node
3560 .isExternal() && ( ( new_x_min < 20 ) || ( _y_distance * node.getNumberOfExternalNodes() < getTreeFontSet()._fm_large
3561 .getHeight() ) ) ) ) ) {
3564 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3565 paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
3568 final private void paintNodeWithRenderableData( final Graphics2D g,
3569 final PhylogenyNode node,
3570 final boolean to_graphics_file,
3571 final boolean to_pdf ) {
3572 if ( isNodeDataInvisible( node ) && !to_graphics_file ) {
3575 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
3578 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
3579 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
3580 RenderableDomainArchitecture rds = null;
3581 if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) {
3583 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
3585 catch ( final ClassCastException cce ) {
3586 cce.printStackTrace();
3588 if ( rds != null ) {
3589 rds.setRenderingHeight( 6 );
3591 if ( getControlPanel().isShowTaxonomyCode()
3592 && ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( node ) ) ) ) {
3593 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " );
3595 if ( getControlPanel().isShowGeneNames()
3596 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
3597 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
3599 if ( getControlPanel().isShowGeneSymbols()
3600 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
3601 x += getTreeFontSet()._fm_large
3602 .stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
3604 if ( getControlPanel().isShowSequenceAcc()
3605 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3606 x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
3610 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3611 x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
3613 rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
3618 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
3619 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
3620 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
3621 getStatisticsForExpressionValues(),
3622 getConfiguration() );
3625 PhylogenyNode my_node = node;
3626 if ( !getControlPanel().isDrawPhylogram() ) {
3627 my_node = getPhylogeny().getFirstExternalNode();
3629 if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
3630 x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
3632 if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
3633 x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
3635 rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
3641 final private void paintOvRectangle( final Graphics2D g ) {
3642 final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
3643 final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
3644 final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
3645 final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
3646 final float width = getOvMaxWidth() / w_ratio;
3647 final float height = getOvMaxHeight() / h_ratio;
3648 final float x = getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / x_ratio;
3649 final float y = getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / y_ratio;
3650 g.setColor( getTreeColorSet().getFoundColor() );
3651 getOvRectangle().setRect( x, y, width, height );
3652 if ( ( width < 6 ) && ( height < 6 ) ) {
3653 drawRectFilled( x, y, 6, 6, g );
3654 getOvVirtualRectangle().setRect( x, y, 6, 6 );
3656 else if ( width < 6 ) {
3657 drawRectFilled( x, y, 6, height, g );
3658 getOvVirtualRectangle().setRect( x, y, 6, height );
3660 else if ( height < 6 ) {
3661 drawRectFilled( x, y, width, 6, g );
3662 getOvVirtualRectangle().setRect( x, y, width, 6 );
3665 drawRect( x, y, width, height, g );
3666 if ( isInOvRect() ) {
3667 drawRect( x + 1, y + 1, width - 2, height - 2, g );
3669 getOvVirtualRectangle().setRect( x, y, width, height );
3673 final void paintPhylogeny( final Graphics2D g,
3674 final boolean to_pdf,
3675 final boolean to_graphics_file,
3676 final int graphics_file_width,
3677 final int graphics_file_height,
3678 final int graphics_file_x,
3679 final int graphics_file_y ) {
3680 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
3683 if ( _control_panel.isShowSequenceRelations() ) {
3684 _query_sequence = _control_panel.getSelectedQuerySequence();
3686 // Color the background
3688 final Rectangle r = getVisibleRect();
3689 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
3690 g.setColor( getTreeColorSet().getBackgroundColor() );
3691 if ( !to_graphics_file ) {
3695 if ( getOptions().isPrintBlackAndWhite() ) {
3696 g.setColor( Color.WHITE );
3698 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
3702 if ( !to_graphics_file ) {
3703 g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
3704 + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
3708 g.setPaint( new GradientPaint( graphics_file_x,
3710 getTreeColorSet().getBackgroundColor(),
3712 graphics_file_y + graphics_file_height,
3713 getTreeColorSet().getBackgroundColorGradientBottom() ) );
3714 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
3717 g.setStroke( new BasicStroke( 1 ) );
3720 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
3722 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
3723 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
3724 _external_node_index = 0;
3725 // Position starting X of tree
3726 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) {
3727 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
3729 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
3730 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot()
3731 .getDistanceToParent() * getXcorrectionFactor() ) ) );
3734 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
3736 // Position starting Y of tree
3737 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
3738 + ( TreePanel.MOVE / 2.0f ) );
3739 final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) );
3740 if ( getControlPanel().isDynamicallyHideData() ) {
3741 if ( dynamic_hiding_factor > 1 ) {
3742 getControlPanel().setDynamicHidingIsOn( true );
3745 getControlPanel().setDynamicHidingIsOn( false );
3748 if ( _nodes_in_preorder == null ) {
3749 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
3751 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3752 _nodes_in_preorder[ i++ ] = it.next();
3755 //final PhylogenyNodeIterator it;
3756 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3757 // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData()
3758 // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
3760 for( int i = 0; i < _nodes_in_preorder.length; ++i ) {
3761 paintNodeRectangular( g, _nodes_in_preorder[ i ], to_pdf, getControlPanel().isDynamicallyHideData()
3762 && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file );
3764 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
3765 if ( !( to_graphics_file || to_pdf ) ) {
3768 getVisibleRect().y + getVisibleRect().height,
3773 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
3776 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3777 paintPhylogenyLite( g );
3780 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
3781 if ( getControlPanel().getDynamicallyHideData() != null ) {
3782 getControlPanel().setDynamicHidingIsOn( false );
3784 final double angle = getStartingAngle();
3785 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
3786 _dynamic_hiding_factor = 0;
3787 if ( getControlPanel().isDynamicallyHideData() ) {
3788 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
3789 .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
3791 if ( getControlPanel().getDynamicallyHideData() != null ) {
3792 if ( _dynamic_hiding_factor > 1 ) {
3793 getControlPanel().setDynamicHidingIsOn( true );
3796 getControlPanel().setDynamicHidingIsOn( false );
3799 paintUnrooted( _phylogeny.getRoot(),
3801 ( float ) ( angle + 2 * Math.PI ),
3806 if ( getOptions().isShowScale() ) {
3807 if ( !( to_graphics_file || to_pdf ) ) {
3810 getVisibleRect().y + getVisibleRect().height,
3815 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
3818 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3819 g.setColor( getTreeColorSet().getOvColor() );
3820 paintUnrootedLite( _phylogeny.getRoot(),
3822 angle + 2 * Math.PI,
3824 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
3825 paintOvRectangle( g );
3828 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3829 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
3830 final int d = radius + MOVE + getLongestExtNodeInfo();
3831 _dynamic_hiding_factor = 0;
3832 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
3833 _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
3834 .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
3836 if ( getControlPanel().getDynamicallyHideData() != null ) {
3837 if ( _dynamic_hiding_factor > 1 ) {
3838 getControlPanel().setDynamicHidingIsOn( true );
3841 getControlPanel().setDynamicHidingIsOn( false );
3844 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
3845 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
3846 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
3847 : getOvMaxWidth() / 2 );
3848 double x_scale = 1.0;
3849 double y_scale = 1.0;
3850 int x_pos = getVisibleRect().x + getOvXPosition();
3851 int y_pos = getVisibleRect().y + getOvYPosition();
3852 if ( getWidth() > getHeight() ) {
3853 x_scale = ( double ) getHeight() / getWidth();
3854 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
3857 y_scale = ( double ) getWidth() / getHeight();
3858 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
3860 _at = g.getTransform();
3861 g.scale( x_scale, y_scale );
3862 paintCircularLite( _phylogeny,
3866 ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
3869 g.setTransform( _at );
3870 paintOvRectangle( g );
3875 final private void paintPhylogenyLite( final Graphics2D g ) {
3876 //System.out.println( getVisibleRect().x + " " + getVisibleRect().y );
3879 .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
3880 .getWidth() ) ) ) );
3881 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
3882 //final PhylogenyNodeIterator it;
3883 //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
3884 // paintNodeLite( g, it.next() );
3886 for( int i = 0; i < _nodes_in_preorder.length; ++i ) {
3887 paintNodeLite( g, _nodes_in_preorder[ i ] );
3889 paintOvRectangle( g );
3893 * Paint the root branch. (Differs from others because it will always be a
3894 * single horizontal line).
3895 * @param to_graphics_file
3897 * @return new x1 value
3899 final private void paintRootBranch( final Graphics2D g,
3902 final PhylogenyNode root,
3903 final boolean to_pdf,
3904 final boolean to_graphics_file ) {
3905 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
3906 float d = getXdistance();
3907 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
3908 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
3910 if ( d < MIN_ROOT_LENGTH ) {
3911 d = MIN_ROOT_LENGTH;
3913 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
3914 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
3917 final double w = PhylogenyMethods.getBranchWidthValue( root );
3918 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
3920 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
3923 final private void paintScale( final Graphics2D g,
3926 final boolean to_pdf,
3927 final boolean to_graphics_file ) {
3929 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
3931 final int y2 = y1 - 8;
3932 final int y3 = y1 - 4;
3933 g.setFont( getTreeFontSet().getSmallFont() );
3934 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3935 g.setColor( Color.BLACK );
3938 g.setColor( getTreeColorSet().getBranchLengthColor() );
3940 drawLine( x1, y1, x1, y2, g );
3941 drawLine( x2, y1, x2, y2, g );
3942 drawLine( x1, y3, x2, y3, g );
3943 if ( getScaleLabel() != null ) {
3944 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
3948 final private int paintTaxonomy( final Graphics2D g,
3949 final PhylogenyNode node,
3950 final boolean is_in_found_nodes,
3951 final boolean to_pdf,
3952 final boolean to_graphics_file,
3953 final double x_shift ) {
3954 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3955 g.setFont( getTreeFontSet().getLargeItalicFont() );
3956 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3957 g.setColor( Color.BLACK );
3959 else if ( is_in_found_nodes ) {
3960 g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
3961 g.setColor( getTreeColorSet().getFoundColor() );
3963 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3964 g.setColor( getTaxonomyBasedColor( node ) );
3966 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
3967 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3968 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3970 else if ( to_pdf ) {
3971 g.setColor( Color.BLACK );
3974 g.setColor( getTreeColorSet().getTaxonomyColor() );
3976 final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
3977 final double start_y = node.getYcoord()
3978 + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
3980 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
3981 _sb.append( taxonomy.getTaxonomyCode() );
3984 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
3985 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
3986 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3987 if ( getOptions().isAbbreviateScientificTaxonNames()
3988 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
3989 abbreviateScientificName( taxonomy.getScientificName() );
3992 _sb.append( taxonomy.getScientificName() );
3995 _sb.append( taxonomy.getCommonName() );
3998 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3999 if ( getOptions().isAbbreviateScientificTaxonNames()
4000 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4001 abbreviateScientificName( taxonomy.getScientificName() );
4004 _sb.append( taxonomy.getScientificName() );
4008 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4009 _sb.append( taxonomy.getCommonName() );
4013 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
4014 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
4015 if ( getOptions().isAbbreviateScientificTaxonNames()
4016 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
4017 abbreviateScientificName( taxonomy.getScientificName() );
4020 _sb.append( taxonomy.getScientificName() );
4025 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
4026 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
4027 _sb.append( taxonomy.getCommonName() );
4031 final String label = _sb.toString();
4033 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
4034 && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) {
4035 // invert font color and background color to show that this is the query sequence
4036 final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
4040 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
4041 g.setColor( getTreeColorSet().getBackgroundColor() );
4044 TreePanel.drawString( label, start_x, start_y, g );
4045 if ( is_in_found_nodes ) {
4046 return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
4049 return getTreeFontSet()._fm_large_italic.stringWidth( label );
4053 private void abbreviateScientificName( final String sn ) {
4054 final String[] a = sn.split( "\\s+" );
4055 _sb.append( a[ 0 ].substring( 0, 1 ) );
4056 _sb.append( a[ 1 ].substring( 0, 2 ) );
4057 if ( a.length > 2 ) {
4058 for( int i = 2; i < a.length; i++ ) {
4060 _sb.append( a[ i ] );
4065 final private void paintUnrooted( final PhylogenyNode n,
4066 final double low_angle,
4067 final double high_angle,
4068 final boolean radial_labels,
4070 final boolean to_pdf,
4071 final boolean to_graphics_file ) {
4073 n.setXcoord( getWidth() / 2 );
4074 n.setYcoord( getHeight() / 2 );
4076 if ( n.isExternal() ) {
4077 paintNodeDataUnrootedCirc( g,
4082 ( high_angle + low_angle ) / 2,
4083 isInFoundNodes( n ) );
4086 final float num_enclosed = n.getNumberOfExternalNodes();
4087 final float x = n.getXcoord();
4088 final float y = n.getYcoord();
4089 double current_angle = low_angle;
4090 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
4091 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
4092 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
4093 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
4094 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4095 final PhylogenyNode desc = n.getChildNode( i );
4096 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
4097 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
4098 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
4099 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
4102 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
4105 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
4108 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4109 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4111 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4112 if ( desc.getDistanceToParent() < 0 ) {
4116 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
4120 length = getUrtFactor();
4122 final double mid_angle = current_angle + arc_size / 2;
4123 final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
4124 final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
4125 desc.setXcoord( new_x );
4126 desc.setYcoord( new_y );
4127 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
4128 current_angle += arc_size;
4129 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
4130 drawLine( x, y, new_x, new_y, g );
4131 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
4134 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
4138 final private void paintUnrootedLite( final PhylogenyNode n,
4139 final double low_angle,
4140 final double high_angle,
4142 final float urt_ov_factor ) {
4144 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() / 2 );
4145 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() / 2 );
4146 n.setXSecondary( x_pos );
4147 n.setYSecondary( y_pos );
4149 if ( n.isExternal() ) {
4152 final float num_enclosed = n.getNumberOfExternalNodes();
4153 final float x = n.getXSecondary();
4154 final float y = n.getYSecondary();
4155 double current_angle = low_angle;
4156 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
4157 final PhylogenyNode desc = n.getChildNode( i );
4158 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
4159 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
4161 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4162 if ( desc.getDistanceToParent() < 0 ) {
4166 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
4170 length = urt_ov_factor;
4172 final double mid_angle = current_angle + arc_size / 2;
4173 final float new_x = ( float ) ( x + Math.cos( mid_angle ) * length );
4174 final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
4175 desc.setXSecondary( new_x );
4176 desc.setYSecondary( new_y );
4177 if ( isInFoundNodes( desc ) ) {
4178 g.setColor( getTreeColorSet().getFoundColor() );
4179 drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
4180 g.setColor( getTreeColorSet().getOvColor() );
4182 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
4183 current_angle += arc_size;
4184 drawLine( x, y, new_x, new_y, g );
4188 final private void pasteSubtree( final PhylogenyNode node ) {
4189 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4190 errorMessageNoCutCopyPasteInUnrootedDisplay();
4193 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
4194 JOptionPane.showMessageDialog( this,
4195 "No tree in buffer (need to copy or cut a subtree first)",
4196 "Attempt to paste with empty buffer",
4197 JOptionPane.ERROR_MESSAGE );
4200 final String label = getASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
4201 final Object[] options = { "As sibling", "As descendant", "Cancel" };
4202 final int r = JOptionPane.showOptionDialog( this,
4203 "How to paste subtree" + label + "?",
4205 JOptionPane.CLOSED_OPTION,
4206 JOptionPane.QUESTION_MESSAGE,
4210 boolean paste_as_sibling = true;
4212 paste_as_sibling = false;
4214 else if ( r != 0 ) {
4217 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
4218 buffer_phy.setAllNodesToNotCollapse();
4219 buffer_phy.preOrderReId();
4220 buffer_phy.setRooted( true );
4221 boolean need_to_show_whole = false;
4222 if ( paste_as_sibling ) {
4223 if ( node.isRoot() ) {
4224 JOptionPane.showMessageDialog( this,
4225 "Cannot paste sibling to root",
4226 "Attempt to paste sibling to root",
4227 JOptionPane.ERROR_MESSAGE );
4230 buffer_phy.addAsSibling( node );
4233 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
4234 need_to_show_whole = true;
4235 _phylogeny = buffer_phy;
4238 buffer_phy.addAsChild( node );
4241 if ( getCopiedAndPastedNodes() == null ) {
4242 setCopiedAndPastedNodes( new HashSet<Integer>() );
4244 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
4245 final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
4246 for( final PhylogenyNode n : nodes ) {
4247 node_ids.add( n.getId() );
4249 node_ids.add( node.getId() );
4250 getCopiedAndPastedNodes().addAll( node_ids );
4251 setNodeInPreorderToNull();
4252 _phylogeny.externalNodesHaveChanged();
4253 _phylogeny.clearHashIdToNodeMap();
4254 _phylogeny.recalculateNumberOfExternalDescendants( true );
4255 resetNodeIdToDistToLeafMap();
4257 if ( need_to_show_whole ) {
4258 getControlPanel().showWhole();
4263 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
4264 throws PrinterException {
4265 if ( page_index > 0 ) {
4266 return ( NO_SUCH_PAGE );
4269 final Graphics2D g2d = ( Graphics2D ) g;
4270 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
4271 // Turn off double buffering !?
4272 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
4273 // Turn double buffering back on !?
4274 return ( PAGE_EXISTS );
4278 final void recalculateMaxDistanceToRoot() {
4279 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
4283 * Remove all edit-node frames
4285 final void removeAllEditNodeJFrames() {
4286 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
4287 if ( _node_frames[ i ] != null ) {
4288 _node_frames[ i ].dispose();
4289 _node_frames[ i ] = null;
4292 _node_frame_index = 0;
4296 * Remove a node-edit frame.
4298 final void removeEditNodeFrame( final int i ) {
4299 _node_frame_index--;
4300 _node_frames[ i ] = null;
4301 if ( i < _node_frame_index ) {
4302 for( int j = 0; j < _node_frame_index - 1; j++ ) {
4303 _node_frames[ j ] = _node_frames[ j + 1 ];
4305 _node_frames[ _node_frame_index ] = null;
4309 final void reRoot( final PhylogenyNode node ) {
4310 if ( !getPhylogeny().isRerootable() ) {
4311 JOptionPane.showMessageDialog( this,
4312 "This is not rerootable",
4314 JOptionPane.WARNING_MESSAGE );
4317 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4318 JOptionPane.showMessageDialog( this,
4319 "Cannot reroot in unrooted display type",
4320 "Attempt to reroot tree in unrooted display",
4321 JOptionPane.WARNING_MESSAGE );
4324 getPhylogeny().reRoot( node );
4325 getPhylogeny().recalculateNumberOfExternalDescendants( true );
4326 resetNodeIdToDistToLeafMap();
4327 setNodeInPreorderToNull();
4328 resetPreferredSize();
4329 getMainPanel().adjustJScrollPane();
4331 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
4332 getControlPanel().showWhole();
4336 final void resetNodeIdToDistToLeafMap() {
4337 _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
4340 final void resetPreferredSize() {
4341 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
4347 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
4348 if ( getControlPanel().isDrawPhylogram() ) {
4350 + getLongestExtNodeInfo()
4352 .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
4355 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4357 + getLongestExtNodeInfo()
4358 + ForesterUtil.roundToInt( getXdistance()
4359 * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
4363 + getLongestExtNodeInfo()
4364 + ForesterUtil.roundToInt( getXdistance()
4365 * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
4368 setPreferredSize( new Dimension( x, y ) );
4371 public final void setArrowCursor() {
4372 setCursor( ARROW_CURSOR );
4376 final void setControlPanel( final ControlPanel atv_control ) {
4377 _control_panel = atv_control;
4380 final private void setCopiedAndPastedNodes( final Set<Integer> nodeIds ) {
4381 getMainPanel().setCopiedAndPastedNodes( nodeIds );
4384 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
4385 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
4388 public final void setEdited( final boolean edited ) {
4392 final void setFoundNodes( final Set<Integer> found_nodes ) {
4393 _found_nodes = found_nodes;
4396 final private void setInOv( final boolean in_ov ) {
4400 final void setInOvRect( final boolean in_ov_rect ) {
4401 _in_ov_rect = in_ov_rect;
4404 final void setLargeFonts() {
4405 getTreeFontSet().largeFonts();
4408 final void setLastMouseDragPointX( final float x ) {
4409 _last_drag_point_x = x;
4412 final void setLastMouseDragPointY( final float y ) {
4413 _last_drag_point_y = y;
4416 final void setLongestExtNodeInfo( final int i ) {
4417 _longest_ext_node_info = i;
4420 final void setMediumFonts() {
4421 getTreeFontSet().mediumFonts();
4424 final private void setOvMaxHeight( final float ov_max_height ) {
4425 _ov_max_height = ov_max_height;
4428 final private void setOvMaxWidth( final float ov_max_width ) {
4429 _ov_max_width = ov_max_width;
4432 final void setOvOn( final boolean ov_on ) {
4436 final private void setOvXcorrectionFactor( final float f ) {
4437 _ov_x_correction_factor = f;
4440 final private void setOvXDistance( final float ov_x_distance ) {
4441 _ov_x_distance = ov_x_distance;
4444 final private void setOvXPosition( final int ov_x_position ) {
4445 _ov_x_position = ov_x_position;
4448 final private void setOvYDistance( final float ov_y_distance ) {
4449 _ov_y_distance = ov_y_distance;
4452 final private void setOvYPosition( final int ov_y_position ) {
4453 _ov_y_position = ov_y_position;
4456 final private void setOvYStart( final int ov_y_start ) {
4457 _ov_y_start = ov_y_start;
4461 * Set parameters for printing the displayed tree
4466 public final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
4467 // updateStyle(); not needed?
4468 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4470 if ( recalc_longest_ext_node_info ) {
4471 calculateLongestExtNodeInfo();
4473 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
4474 final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
4475 if ( ext_nodes == 1 ) {
4476 ext_nodes = max_depth;
4477 if ( ext_nodes < 1 ) {
4484 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
4485 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
4486 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
4489 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
4490 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
4492 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
4493 if ( xdist < 0.0 ) {
4496 if ( ov_xdist < 0.0 ) {
4499 if ( ydist < 0.0 ) {
4502 setXdistance( xdist );
4503 setYdistance( ydist );
4504 setOvXDistance( ov_xdist );
4505 final double height = _phylogeny.getHeight();
4507 final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height );
4508 setXcorrectionFactor( corr > 0 ? corr : 0 );
4509 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
4510 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
4513 setXcorrectionFactor( 0 );
4514 setOvXcorrectionFactor( 0 );
4516 _circ_max_depth = max_depth;
4521 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
4522 _graphics_type = graphics_type;
4526 final private void setScaleDistance( final double scale_distance ) {
4527 _scale_distance = scale_distance;
4530 final private void setScaleLabel( final String scale_label ) {
4531 _scale_label = scale_label;
4534 final void setSmallFonts() {
4535 getTreeFontSet().smallFonts();
4538 final void setStartingAngle( final double starting_angle ) {
4539 _urt_starting_angle = starting_angle;
4542 final void setSuperTinyFonts() {
4543 getTreeFontSet().superTinyFonts();
4546 final void setTextAntialias() {
4547 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4548 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
4549 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
4552 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
4555 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
4556 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
4557 && !getMainPanel().getOptions().isShowDefaultNodeShapes()
4558 && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
4559 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
4562 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
4565 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
4566 RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
4568 catch ( final Throwable e ) {
4569 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
4573 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
4574 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
4578 final void setTinyFonts() {
4579 getTreeFontSet().tinyFonts();
4583 * Set a phylogeny tree.
4586 * an instance of a Phylogeny
4588 public final void setTree( final Phylogeny t ) {
4589 setNodeInPreorderToNull();
4593 final void setNodeInPreorderToNull() {
4594 _nodes_in_preorder = null;
4597 final void setTreeFile( final File treefile ) {
4598 _treefile = treefile;
4601 final private void setUpUrtFactor() {
4602 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4603 : getVisibleRect().height;
4604 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4605 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4608 final int max_depth = _circ_max_depth;
4609 if ( max_depth > 0 ) {
4610 setUrtFactor( d / ( 2 * max_depth ) );
4613 setUrtFactor( d / 2 );
4616 setUrtFactorOv( getUrtFactor() );
4619 final private void setUrtFactor( final float urt_factor ) {
4620 _urt_factor = urt_factor;
4623 final private void setUrtFactorOv( final float urt_factor_ov ) {
4624 _urt_factor_ov = urt_factor_ov;
4627 public final void setWaitCursor() {
4628 setCursor( WAIT_CURSOR );
4632 final void setXcorrectionFactor( final float f ) {
4633 _x_correction_factor = f;
4636 final void setXdistance( final float x ) {
4640 final void setYdistance( final float y ) {
4644 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
4646 if ( ( node.getName().length() > 0 )
4647 || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
4648 || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
4649 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
4650 || node.getBranchData().isHasConfidences() ) {
4651 _popup_buffer.setLength( 0 );
4653 if ( node.getName().length() > 0 ) {
4655 _popup_buffer.append( node.getName() );
4657 if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
4659 boolean enc_data = false;
4660 final Taxonomy tax = node.getNodeData().getTaxonomy();
4661 if ( _popup_buffer.length() > 0 ) {
4662 _popup_buffer.append( "\n" );
4664 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
4665 _popup_buffer.append( "[" );
4666 _popup_buffer.append( tax.getTaxonomyCode() );
4667 _popup_buffer.append( "]" );
4670 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
4672 _popup_buffer.append( " " );
4674 _popup_buffer.append( tax.getScientificName() );
4677 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
4679 _popup_buffer.append( " (" );
4682 _popup_buffer.append( "(" );
4684 _popup_buffer.append( tax.getCommonName() );
4685 _popup_buffer.append( ")" );
4688 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
4690 _popup_buffer.append( " (" );
4693 _popup_buffer.append( "(" );
4695 _popup_buffer.append( tax.getAuthority() );
4696 _popup_buffer.append( ")" );
4699 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
4701 _popup_buffer.append( " [" );
4704 _popup_buffer.append( "[" );
4706 _popup_buffer.append( tax.getRank() );
4707 _popup_buffer.append( "]" );
4710 if ( tax.getSynonyms().size() > 0 ) {
4712 _popup_buffer.append( " " );
4714 _popup_buffer.append( "[" );
4716 for( final String syn : tax.getSynonyms() ) {
4717 if ( !ForesterUtil.isEmpty( syn ) ) {
4719 _popup_buffer.append( syn );
4720 if ( counter < tax.getSynonyms().size() ) {
4721 _popup_buffer.append( ", " );
4726 _popup_buffer.append( "]" );
4729 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
4730 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
4731 _popup_buffer.append( "[" );
4732 _popup_buffer.append( tax.getIdentifier().getProvider() );
4733 _popup_buffer.append( "] " );
4735 _popup_buffer.append( tax.getIdentifier().getValue() );
4739 if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
4741 boolean enc_data = false;
4742 if ( _popup_buffer.length() > 0 ) {
4743 _popup_buffer.append( "\n" );
4745 final Sequence seq = node.getNodeData().getSequence();
4746 if ( seq.getAccession() != null ) {
4747 _popup_buffer.append( "[" );
4748 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
4749 _popup_buffer.append( seq.getAccession().getSource() );
4750 _popup_buffer.append( ":" );
4752 _popup_buffer.append( seq.getAccession().getValue() );
4753 _popup_buffer.append( "]" );
4756 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
4758 _popup_buffer.append( " [" );
4761 _popup_buffer.append( "[" );
4763 _popup_buffer.append( seq.getSymbol() );
4764 _popup_buffer.append( "]" );
4767 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
4769 _popup_buffer.append( " " );
4771 _popup_buffer.append( seq.getName() );
4774 if ( node.getNodeData().isHasDate() ) {
4776 if ( _popup_buffer.length() > 0 ) {
4777 _popup_buffer.append( "\n" );
4779 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
4781 if ( node.getNodeData().isHasDistribution() ) {
4783 if ( _popup_buffer.length() > 0 ) {
4784 _popup_buffer.append( "\n" );
4786 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
4788 if ( node.getBranchData().isHasConfidences() ) {
4789 final List<Confidence> confs = node.getBranchData().getConfidences();
4790 for( final Confidence confidence : confs ) {
4792 if ( _popup_buffer.length() > 0 ) {
4793 _popup_buffer.append( "\n" );
4795 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
4796 _popup_buffer.append( "[" );
4797 _popup_buffer.append( confidence.getType() );
4798 _popup_buffer.append( "] " );
4801 .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
4803 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
4804 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4805 _popup_buffer.append( " (sd=" );
4806 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
4807 .getStandardDeviation(), getOptions()
4808 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
4809 _popup_buffer.append( ")" );
4813 if ( node.getNodeData().isHasProperties() ) {
4814 final PropertiesMap properties = node.getNodeData().getProperties();
4815 for( final String ref : properties.getPropertyRefs() ) {
4816 _popup_buffer.append( "\n" );
4817 final Property p = properties.getProperty( ref );
4818 _popup_buffer.append( getPartAfterColon( p.getRef() ) );
4819 _popup_buffer.append( "=" );
4820 _popup_buffer.append( p.getValue() );
4821 if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
4822 _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
4826 if ( _popup_buffer.length() > 0 ) {
4827 if ( !getConfiguration().isUseNativeUI() ) {
4829 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
4830 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
4831 if ( isInFoundNodes( node ) ) {
4832 _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
4834 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
4835 _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
4838 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
4842 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
4844 _rollover_popup.setText( _popup_buffer.toString() );
4845 _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null,
4847 e.getLocationOnScreen().x + 10,
4848 e.getLocationOnScreen().y
4850 _node_desc_popup.show();
4854 catch ( final Exception ex ) {
4859 final private void showNodeEditFrame( final PhylogenyNode n ) {
4860 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4861 // pop up edit box for single node
4862 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
4863 _node_frame_index++;
4866 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4870 final private void showNodeFrame( final PhylogenyNode n ) {
4871 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4872 // pop up edit box for single node
4873 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
4874 _node_frame_index++;
4877 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4881 final void subTree( final PhylogenyNode node ) {
4882 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4883 JOptionPane.showMessageDialog( this,
4884 "Cannot get a sub/super tree in unrooted display",
4885 "Attempt to get sub/super tree in unrooted display",
4886 JOptionPane.WARNING_MESSAGE );
4889 if ( node.isExternal() ) {
4890 JOptionPane.showMessageDialog( this,
4891 "Cannot get a subtree of a external node",
4892 "Attempt to get subtree of external node",
4893 JOptionPane.WARNING_MESSAGE );
4896 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
4897 JOptionPane.showMessageDialog( this,
4898 "Cannot get a subtree of the root node",
4899 "Attempt to get subtree of root node",
4900 JOptionPane.WARNING_MESSAGE );
4903 setNodeInPreorderToNull();
4904 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
4905 _sub_phylogenies[ _subtree_index ] = _phylogeny;
4906 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
4908 _phylogeny = subTree( node, _phylogeny );
4909 updateSubSuperTreeButton();
4911 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
4914 _main_panel.getControlPanel().showWhole();
4918 final boolean isCurrentTreeIsSubtree() {
4919 return ( _subtree_index > 0 );
4922 final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
4923 final Phylogeny new_phy = new Phylogeny();
4924 new_phy.setRooted( true );
4925 new_phy.setName( source_phy.getName() );
4926 new_phy.setDescription( source_phy.getDescription() );
4927 new_phy.setType( source_phy.getType() );
4928 new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
4929 new_phy.setConfidence( source_phy.getConfidence() );
4930 new_phy.setIdentifier( source_phy.getIdentifier() );
4931 new_phy.setRoot( new_root.copyNodeDataShallow() );
4933 for( final PhylogenyNode n : new_root.getDescendants() ) {
4934 new_phy.getRoot().setChildNode( i++, n );
4939 final void superTree() {
4940 setNodeInPreorderToNull();
4941 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
4942 for( final PhylogenyNode n : temp_root.getDescendants() ) {
4943 n.setParent( temp_root );
4945 _sub_phylogenies[ _subtree_index ] = null;
4946 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
4947 _phylogeny = _sub_phylogenies[ --_subtree_index ];
4948 updateSubSuperTreeButton();
4951 final void swap( final PhylogenyNode node ) {
4952 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
4955 if ( node.getNumberOfDescendants() > 2 ) {
4956 JOptionPane.showMessageDialog( this,
4957 "Cannot swap descendants of nodes with more than 2 descendants",
4958 "Cannot swap descendants",
4959 JOptionPane.ERROR_MESSAGE );
4962 if ( !node.isExternal() ) {
4963 node.swapChildren();
4964 setNodeInPreorderToNull();
4965 _phylogeny.externalNodesHaveChanged();
4966 _phylogeny.clearHashIdToNodeMap();
4967 _phylogeny.recalculateNumberOfExternalDescendants( true );
4968 resetNodeIdToDistToLeafMap();
4974 final void sortDescendants( final PhylogenyNode node ) {
4975 if ( !node.isExternal() ) {
4976 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
4977 if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
4978 .isShowTaxonomyCommonNames() ) ) {
4979 if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
4980 .isShowGeneSymbols() ) ) {
4981 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
4983 else if ( getControlPanel().isShowNodeNames() ) {
4984 pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
4987 PhylogenyMethods.sortNodeDescendents( node, pri );
4988 setNodeInPreorderToNull();
4989 _phylogeny.externalNodesHaveChanged();
4990 _phylogeny.clearHashIdToNodeMap();
4991 _phylogeny.recalculateNumberOfExternalDescendants( true );
4992 resetNodeIdToDistToLeafMap();
4998 final private void switchDisplaygetPhylogenyGraphicsType() {
4999 switch ( getPhylogenyGraphicsType() ) {
5001 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5002 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
5005 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5006 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
5009 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5010 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
5013 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5014 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
5017 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5018 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
5021 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5022 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5025 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5026 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
5029 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5030 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
5033 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
5035 if ( getControlPanel().getDynamicallyHideData() != null ) {
5036 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5037 getControlPanel().getDynamicallyHideData().setEnabled( false );
5040 getControlPanel().getDynamicallyHideData().setEnabled( true );
5043 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5044 getControlPanel().setDrawPhylogramEnabled( true );
5047 getControlPanel().setDrawPhylogramEnabled( false );
5049 if ( getMainPanel().getMainFrame() == null ) {
5050 // Must be "E" applet version.
5051 ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
5052 .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5055 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
5059 final void taxColor() {
5060 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
5064 AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
5065 _control_panel.setColorBranches( true );
5066 if ( _control_panel.getColorBranchesCb() != null ) {
5067 _control_panel.getColorBranchesCb().setSelected( true );
5073 final void updateOvSettings() {
5074 switch ( getOptions().getOvPlacement() ) {
5076 setOvXPosition( OV_BORDER );
5077 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
5078 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
5081 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
5082 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
5083 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
5086 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
5087 setOvYPosition( OV_BORDER );
5088 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
5091 setOvXPosition( OV_BORDER );
5092 setOvYPosition( OV_BORDER );
5093 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
5098 final void updateOvSizes() {
5099 if ( ( getWidth() > 1.05 * getVisibleRect().width ) || ( getHeight() > 1.05 * getVisibleRect().height ) ) {
5101 float l = getLongestExtNodeInfo();
5102 final float w_ratio = getOvMaxWidth() / getWidth();
5104 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
5105 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
5107 if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
5108 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
5111 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
5113 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
5114 if ( ov_xdist < 0.0 ) {
5117 if ( ydist < 0.0 ) {
5120 setOvXDistance( ov_xdist );
5121 final double height = _phylogeny.getHeight();
5123 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
5124 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
5127 setOvXcorrectionFactor( 0 );
5135 final void updateSubSuperTreeButton() {
5136 if ( _subtree_index < 1 ) {
5137 getControlPanel().deactivateButtonToReturnToSuperTree();
5140 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
5144 final void zoomInDomainStructure() {
5145 if ( _domain_structure_width < 2000 ) {
5146 _domain_structure_width *= 1.2;
5150 final void zoomOutDomainStructure() {
5151 if ( _domain_structure_width > 20 ) {
5152 _domain_structure_width *= 0.8;
5156 final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
5157 g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5160 final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
5161 g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
5164 final private static boolean isSequenceEmpty( final Sequence seq ) {
5165 return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
5166 && ForesterUtil.isEmpty( seq.getSymbol() );
5169 final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
5170 return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
5171 && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
5172 .getSynonyms().isEmpty() );
5175 final private static boolean plusPressed( final int key_code ) {
5176 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
5177 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
5180 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
5181 _statistics_for_vector_data = statistics_for_expression_values;
5184 DescriptiveStatistics getStatisticsForExpressionValues() {
5185 return _statistics_for_vector_data;
5188 final private class SubtreeColorizationActionListener implements ActionListener {
5190 JColorChooser _chooser;
5191 PhylogenyNode _node;
5193 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
5199 public void actionPerformed( final ActionEvent e ) {
5200 final Color c = _chooser.getColor();
5202 colorizeSubtree( c, _node );
5207 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
5208 getMainPanel().setImageMap( image_map );
5211 public synchronized Hashtable<String, BufferedImage> getImageMap() {
5212 return getMainPanel().getImageMap();