2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx;
28 import java.awt.BasicStroke;
29 import java.awt.Color;
30 import java.awt.Cursor;
31 import java.awt.Dimension;
33 import java.awt.FontMetrics;
34 import java.awt.GradientPaint;
35 import java.awt.Graphics;
36 import java.awt.Graphics2D;
37 import java.awt.Point;
38 import java.awt.Rectangle;
39 import java.awt.RenderingHints;
40 import java.awt.Stroke;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.FocusAdapter;
44 import java.awt.event.FocusEvent;
45 import java.awt.event.InputEvent;
46 import java.awt.event.KeyAdapter;
47 import java.awt.event.KeyEvent;
48 import java.awt.event.MouseEvent;
49 import java.awt.event.MouseWheelEvent;
50 import java.awt.event.MouseWheelListener;
51 import java.awt.font.FontRenderContext;
52 import java.awt.font.TextAttribute;
53 import java.awt.font.TextLayout;
54 import java.awt.geom.AffineTransform;
55 import java.awt.geom.Arc2D;
56 import java.awt.geom.CubicCurve2D;
57 import java.awt.geom.Ellipse2D;
58 import java.awt.geom.Line2D;
59 import java.awt.geom.Path2D;
60 import java.awt.geom.QuadCurve2D;
61 import java.awt.geom.Rectangle2D;
62 import java.awt.image.BufferedImage;
63 import java.awt.print.PageFormat;
64 import java.awt.print.Printable;
65 import java.awt.print.PrinterException;
67 import java.io.IOException;
68 import java.io.UnsupportedEncodingException;
70 import java.net.URISyntaxException;
71 import java.net.URLEncoder;
72 import java.text.AttributedString;
73 import java.text.DecimalFormat;
74 import java.text.DecimalFormatSymbols;
75 import java.text.NumberFormat;
76 import java.util.ArrayList;
77 import java.util.Collections;
78 import java.util.HashMap;
79 import java.util.HashSet;
80 import java.util.Hashtable;
81 import java.util.Iterator;
82 import java.util.List;
85 import java.util.SortedSet;
87 import javax.swing.BorderFactory;
88 import javax.swing.JColorChooser;
89 import javax.swing.JDialog;
90 import javax.swing.JMenuItem;
91 import javax.swing.JOptionPane;
92 import javax.swing.JPanel;
93 import javax.swing.JPopupMenu;
94 import javax.swing.JTextArea;
95 import javax.swing.Popup;
96 import javax.swing.PopupFactory;
98 import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON;
99 import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
100 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
101 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
102 import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
103 import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
104 import org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence;
105 import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
106 import org.forester.archaeopteryx.tools.Blast;
107 import org.forester.archaeopteryx.tools.ImageLoader;
108 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
109 import org.forester.io.writers.SequenceWriter;
110 import org.forester.phylogeny.Phylogeny;
111 import org.forester.phylogeny.PhylogenyMethods;
112 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
113 import org.forester.phylogeny.PhylogenyNode;
114 import org.forester.phylogeny.data.Accession;
115 import org.forester.phylogeny.data.Annotation;
116 import org.forester.phylogeny.data.BranchColor;
117 import org.forester.phylogeny.data.Confidence;
118 import org.forester.phylogeny.data.DomainArchitecture;
119 import org.forester.phylogeny.data.Event;
120 import org.forester.phylogeny.data.NodeDataField;
121 import org.forester.phylogeny.data.NodeVisualData;
122 import org.forester.phylogeny.data.NodeVisualData.NodeFill;
123 import org.forester.phylogeny.data.NodeVisualData.NodeShape;
124 import org.forester.phylogeny.data.PhylogenyDataUtil;
125 import org.forester.phylogeny.data.ProteinDomain;
126 import org.forester.phylogeny.data.Sequence;
127 import org.forester.phylogeny.data.SequenceRelation;
128 import org.forester.phylogeny.data.Taxonomy;
129 import org.forester.phylogeny.data.Uri;
130 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
131 import org.forester.phylogeny.iterators.PreorderTreeIterator;
132 import org.forester.util.DescriptiveStatistics;
133 import org.forester.util.ForesterConstants;
134 import org.forester.util.ForesterUtil;
135 import org.forester.util.SequenceAccessionTools;
136 import org.forester.util.TaxonomyUtil;
138 public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
140 final private class NodeColorizationActionListener implements ActionListener {
142 List<PhylogenyNode> _additional_nodes = null;
143 JColorChooser _chooser = null;
144 PhylogenyNode _node = null;
146 NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
151 NodeColorizationActionListener( final JColorChooser chooser,
152 final PhylogenyNode node,
153 final List<PhylogenyNode> additional_nodes ) {
156 _additional_nodes = additional_nodes;
160 public void actionPerformed( final ActionEvent e ) {
161 final Color c = _chooser.getColor();
163 colorizeNodes( c, _node, _additional_nodes );
168 final private class SubtreeColorizationActionListener implements ActionListener {
170 List<PhylogenyNode> _additional_nodes = null;
171 JColorChooser _chooser = null;
172 PhylogenyNode _node = null;
174 SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
179 SubtreeColorizationActionListener( final JColorChooser chooser,
180 final PhylogenyNode node,
181 final List<PhylogenyNode> additional_nodes ) {
184 _additional_nodes = additional_nodes;
188 public void actionPerformed( final ActionEvent e ) {
189 final Color c = _chooser.getColor();
191 colorizeSubtree( c, _node, _additional_nodes );
195 public final static boolean SPECIAL_DOMAIN_COLORING = true;
196 final static Cursor ARROW_CURSOR = Cursor
197 .getPredefinedCursor( Cursor.DEFAULT_CURSOR );
198 final static Cursor CUT_CURSOR = Cursor
199 .getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
200 final static Cursor HAND_CURSOR = Cursor
201 .getPredefinedCursor( Cursor.HAND_CURSOR );
202 final static Cursor MOVE_CURSOR = Cursor
203 .getPredefinedCursor( Cursor.MOVE_CURSOR );
204 final static Cursor WAIT_CURSOR = Cursor
205 .getPredefinedCursor( Cursor.WAIT_CURSOR );
206 final private static double _180_OVER_PI = 180.0 / Math.PI;
207 private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI
209 private final static int CONFIDENCE_LEFT_MARGIN = 4;
210 private final static int EURO_D = 10;
211 private final static NumberFormat FORMATTER_BRANCH_LENGTH;
212 private final static NumberFormat FORMATTER_CONFIDENCE;
213 private static final float HALF_PI = ( float ) ( Math.PI
215 private final static int LIMIT_FOR_HQ_RENDERING = 2000;
216 private final static int MAX_NODE_FRAMES = 10;
217 private final static int MAX_SUBTREES = 100;
218 private final static int MIN_ROOT_LENGTH = 3;
219 private final static int MOVE = 20;
220 private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
221 private static final float ONEHALF_PI = ( float ) ( 1.5
223 private static final short OV_BORDER = 10;
224 private final static double OVERVIEW_FOUND_NODE_BOX_SIZE = 2;
225 private final static double OVERVIEW_FOUND_NODE_BOX_SIZE_HALF = 1;
226 private static final float PI = ( float ) ( Math.PI );
227 final private static Font POPUP_FONT = new Font( Configuration
228 .getDefaultFontFamilyName(), Font.PLAIN, 12 );
229 private static final float ROUNDED_D = 8;
230 private final static long serialVersionUID = -978349745916505029L;
231 private static final BasicStroke STROKE_0025 = new BasicStroke( 0.025f );
232 private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
233 private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
234 private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
235 private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
236 private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
237 private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
238 private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
239 private static final BasicStroke STROKE_01_DASHED = new BasicStroke( 0.1f,
240 BasicStroke.CAP_SQUARE,
241 BasicStroke.JOIN_ROUND,
246 private static final BasicStroke STROKE_005_DASHED = new BasicStroke( 0.05f,
247 BasicStroke.CAP_SQUARE,
248 BasicStroke.JOIN_ROUND,
253 private static final BasicStroke STROKE_001_DASHED = new BasicStroke( 0.01f,
254 BasicStroke.CAP_SQUARE,
255 BasicStroke.JOIN_ROUND,
260 private static final double TWO_PI = 2 * Math.PI;
261 private final static int WIGGLE = 2;
262 private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me
263 HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
264 final private Arc2D _arc = new Arc2D.Double();
265 private AffineTransform _at;
266 private int _circ_max_depth;
267 final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
268 private JColorChooser _color_chooser = null;
269 private Configuration _configuration = null;
270 private ControlPanel _control_panel = null;
271 private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
272 private Set<Long> _current_external_nodes = null;
273 private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
274 private int _current_external_nodes_data_buffer_change_counter = 0;
275 private int _domain_structure_e_value_thr_exp = AptxConstants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
276 private double _domain_structure_width = AptxConstants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
277 private int _dynamic_hiding_factor = 0;
278 private boolean _edited = false;
279 private final Ellipse2D _ellipse = new Ellipse2D.Float();
280 private int _external_node_index = 0;
281 private Set<Long> _found_nodes_0 = null;
282 private Set<Long> _found_nodes_1 = null;
283 private final FontRenderContext _frc = new FontRenderContext( null,
286 private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
287 private PhylogenyNode _highlight_node = null;
288 private boolean _in_ov = false;
289 private boolean _in_ov_rect = false;
290 private float _last_drag_point_x = 0;
291 private float _last_drag_point_y = 0;
292 private final Line2D _line = new Line2D.Float();
293 private int _longest_ext_node_info = 0;
294 private PhylogenyNode _ext_node_with_longest_txt_info = null;
295 private MainPanel _main_panel = null;
296 private double _max_distance_to_root = -1;
297 private Popup _node_desc_popup;
298 private int _node_frame_index = 0;
299 private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
300 private JPopupMenu _node_popup_menu = null;
301 private JMenuItem _node_popup_menu_items[] = null;
302 private PhylogenyNode[] _nodes_in_preorder = null;
303 private Options _options = null;
304 private float _ov_max_height = 0;
305 private float _ov_max_width = 0;
306 private boolean _ov_on = false;
307 private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
308 private final Rectangle _ov_virtual_rectangle = new Rectangle();
309 private float _ov_x_correction_factor = 0.0f;
310 private float _ov_x_distance = 0;
311 private int _ov_x_position = 0;
312 private float _ov_y_distance = 0;
313 private int _ov_y_position = 0;
314 private int _ov_y_start = 0;
315 private final boolean _phy_has_branch_lengths;
316 private Phylogeny _phylogeny = null;
317 private final Path2D.Float _polygon = new Path2D.Float();
318 private final StringBuffer _popup_buffer = new StringBuffer();
319 private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
320 private Sequence _query_sequence = null;
321 private final Rectangle2D _rectangle = new Rectangle2D.Float();
322 private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
323 RenderingHints.VALUE_RENDER_DEFAULT );
324 private JTextArea _rollover_popup;
325 private PhylogenyNode _root;
326 private final StringBuilder _sb = new StringBuilder();
327 private double _scale_distance = 0.0;
328 private String _scale_label = null;
329 private DescriptiveStatistics _statistics_for_vector_data;
330 private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
331 private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
332 private int _subtree_index = 0;
333 private File _treefile = null;
334 private float _urt_factor = 1;
335 private float _urt_factor_ov = 1;
336 final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
337 final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
338 private double _urt_starting_angle = ( float ) ( Math.PI
340 private float _x_correction_factor = 0.0f;
341 private float _x_distance = 0.0f;
342 private float _y_distance = 0.0f;
343 private int _length_of_longest_text;
344 private int _longest_domain;
345 private Map<String, AttributedString> _attributed_string_map = null;
346 private int _depth_collapse_level = -1;
347 private int _rank_collapse_level = -1;
349 final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
350 dfs.setDecimalSeparator( '.' );
351 FORMATTER_CONFIDENCE = new DecimalFormat( "#.###", dfs );
352 FORMATTER_BRANCH_LENGTH = new DecimalFormat( "#.###", dfs );
355 TreePanel( final Phylogeny t, final Configuration configuration, final MainPanel tjp ) {
356 requestFocusInWindow();
357 addKeyListener( new KeyAdapter() {
360 public void keyPressed( final KeyEvent key_event ) {
361 keyPressedCalls( key_event );
362 requestFocusInWindow();
365 addFocusListener( new FocusAdapter() {
368 public void focusGained( final FocusEvent e ) {
369 requestFocusInWindow();
372 if ( ( t == null ) || t.isEmpty() ) {
373 throw new IllegalArgumentException( "attempt to draw phylogeny which is null or empty" );
375 _graphics_type = tjp.getOptions().getPhylogenyGraphicsType();
377 _configuration = configuration;
379 _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
381 // if ( !_phylogeny.isEmpty() ) {
382 _phylogeny.recalculateNumberOfExternalDescendants( true );
384 setBackground( getTreeColorSet().getBackgroundColor() );
385 final MouseListener mouse_listener = new MouseListener( this );
386 addMouseListener( mouse_listener );
387 addMouseMotionListener( mouse_listener );
388 addMouseWheelListener( this );
389 calculateScaleDistance();
390 FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
391 FORMATTER_BRANCH_LENGTH
392 .setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() );
396 final public void actionPerformed( final ActionEvent e ) {
397 boolean done = false;
398 final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
399 for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
400 // NOTE: index corresponds to the indices of click-to options
401 // in the control panel.
402 if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) {
403 // Set this as the new default click-to action
404 _main_panel.getControlPanel().setClickToAction( index );
405 final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu
406 .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY );
407 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
412 requestFocusInWindow();
415 public synchronized Hashtable<String, BufferedImage> getImageMap() {
416 return getMainPanel().getImageMap();
419 final public MainPanel getMainPanel() {
424 * Get a pointer to the phylogeny
426 * @return a pointer to the phylogeny
428 public final Phylogeny getPhylogeny() {
432 public final TreeColorSet getTreeColorSet() {
433 return getMainPanel().getTreeColorSet();
437 final public void mouseWheelMoved( final MouseWheelEvent e ) {
438 final int notches = e.getWheelRotation();
439 if ( inOvVirtualRectangle( e ) ) {
440 if ( !isInOvRect() ) {
446 if ( isInOvRect() ) {
447 setInOvRect( false );
451 if ( e.isControlDown() && e.isShiftDown() ) {
453 getTreeFontSet().increaseFontSize();
456 getTreeFontSet().decreaseFontSize( 1, false );
458 getControlPanel().displayedPhylogenyMightHaveChanged( true );
459 resetPreferredSize();
463 else if ( e.isShiftDown() && e.isAltDown() ) {
465 for( int i = 0; i < ( -notches ); ++i ) {
466 getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, AptxConstants.WHEEL_ZOOM_IN_FACTOR );
467 getControlPanel().displayedPhylogenyMightHaveChanged( false );
471 for( int i = 0; i < notches; ++i ) {
472 getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
473 AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
474 getControlPanel().displayedPhylogenyMightHaveChanged( false );
478 else if ( e.isShiftDown() ) {
479 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
480 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
482 for( int i = 0; i < ( -notches ); ++i ) {
483 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
484 getControlPanel().displayedPhylogenyMightHaveChanged( false );
488 for( int i = 0; i < notches; ++i ) {
489 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
490 if ( getStartingAngle() < 0 ) {
491 setStartingAngle( TWO_PI + getStartingAngle() );
493 getControlPanel().displayedPhylogenyMightHaveChanged( false );
499 for( int i = 0; i < ( -notches ); ++i ) {
500 getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
501 getControlPanel().displayedPhylogenyMightHaveChanged( false );
505 for( int i = 0; i < notches; ++i ) {
506 getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
507 getControlPanel().displayedPhylogenyMightHaveChanged( false );
514 for( int i = 0; i < ( -notches ); ++i ) {
515 getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
516 AptxConstants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR );
517 getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
518 getControlPanel().displayedPhylogenyMightHaveChanged( false );
522 for( int i = 0; i < notches; ++i ) {
523 getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
524 getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
525 AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
526 getControlPanel().displayedPhylogenyMightHaveChanged( false );
531 requestFocusInWindow();
536 final public void paintComponent( final Graphics g ) {
537 final Graphics2D g2d = ( Graphics2D ) g;
538 g2d.setRenderingHints( _rendering_hints );
539 paintPhylogeny( g2d, false, false, 0, 0, 0, 0 );
543 final public int print( final Graphics g, final PageFormat page_format, final int page_index )
544 throws PrinterException {
545 if ( page_index > 0 ) {
546 return ( NO_SUCH_PAGE );
549 final Graphics2D g2d = ( Graphics2D ) g;
550 g2d.translate( page_format.getImageableX(), page_format.getImageableY() );
551 // Turn off double buffering !?
552 paintPhylogeny( g2d, true, false, 0, 0, 0, 0 );
553 // Turn double buffering back on !?
554 return ( PAGE_EXISTS );
558 public final void setEdited( final boolean edited ) {
562 public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
563 getMainPanel().setImageMap( image_map );
567 * Set a phylogeny tree.
570 * an instance of a Phylogeny
572 public final void setTree( final Phylogeny t ) {
573 setNodeInPreorderToNull();
577 public final void setWaitCursor() {
578 setCursor( WAIT_CURSOR );
583 public void update( final Graphics g ) {
587 private void abbreviateScientificName( final String sn, final StringBuilder sb ) {
588 final String[] a = sn.split( "\\s+" );
589 sb.append( a[ 0 ].substring( 0, 1 ) );
590 sb.append( a[ 1 ].substring( 0, 2 ) );
591 if ( a.length > 2 ) {
592 for( int i = 2; i < a.length; i++ ) {
599 final private void addEmptyNode( final PhylogenyNode node ) {
600 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
601 errorMessageNoCutCopyPasteInUnrootedDisplay();
604 final String label = createASimpleTextRepresentationOfANode( node );
606 if ( ForesterUtil.isEmpty( label ) ) {
607 msg = "How to add the new, empty node?";
610 msg = "How to add the new, empty node to node" + label + "?";
612 final Object[] options = { "As sibling", "As descendant", "Cancel" };
613 final int r = JOptionPane.showOptionDialog( this,
615 "Addition of Empty New Node",
616 JOptionPane.CLOSED_OPTION,
617 JOptionPane.QUESTION_MESSAGE,
621 boolean add_as_sibling = true;
623 add_as_sibling = false;
628 final Phylogeny phy = new Phylogeny();
629 phy.setRoot( new PhylogenyNode() );
630 phy.setRooted( true );
631 if ( add_as_sibling ) {
632 if ( node.isRoot() ) {
633 JOptionPane.showMessageDialog( this,
634 "Cannot add sibling to root",
635 "Attempt to add sibling to root",
636 JOptionPane.ERROR_MESSAGE );
639 phy.addAsSibling( node );
642 phy.addAsChild( node );
644 setNodeInPreorderToNull();
645 _phylogeny.externalNodesHaveChanged();
646 _phylogeny.clearHashIdToNodeMap();
647 _phylogeny.recalculateNumberOfExternalDescendants( true );
648 resetNodeIdToDistToLeafMap();
653 final private void addToCurrentExternalNodes( final long i ) {
654 if ( _current_external_nodes == null ) {
655 _current_external_nodes = new HashSet<Long>();
657 _current_external_nodes.add( i );
660 final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node,
661 final boolean is_vertical,
663 final boolean to_pdf,
664 final boolean to_graphics_file ) {
665 final NodeClickAction action = _control_panel.getActionWhenNodeClicked();
666 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
667 g.setColor( Color.BLACK );
669 else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE )
670 || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE )
671 || ( action == NodeClickAction.ADD_NEW_NODE ) ) && ( getCutOrCopiedTree() != null )
672 && ( getCopiedAndPastedNodes() != null ) && !to_pdf && !to_graphics_file
673 && getCopiedAndPastedNodes().contains( node.getId() ) ) {
674 g.setColor( getTreeColorSet().getFoundColor0() );
676 else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
677 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
680 g.setColor( getTreeColorSet().getBranchColorForPdf() );
683 g.setColor( getTreeColorSet().getBranchColor() );
687 final private void blast( final PhylogenyNode node ) {
688 if ( !isCanBlast( node ) ) {
689 JOptionPane.showMessageDialog( this,
690 "Insufficient information present",
692 JOptionPane.INFORMATION_MESSAGE );
696 final String query = Blast.obtainQueryForBlast( node );
697 System.out.println( "query for BLAST is: " + query );
699 if ( !ForesterUtil.isEmpty( query ) ) {
700 if ( node.getNodeData().isHasSequence() ) {
701 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) {
702 if ( node.getNodeData().getSequence().getType().toLowerCase()
703 .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) {
710 else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
712 .seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) {
721 if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
729 Blast.openNcbiBlastWeb( query, type == 'n', this );
731 catch ( final Exception e ) {
738 private final int calcDynamicHidingFactor() {
739 return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().getHeight() / ( 1.5 * getYdistance() ) ) );
742 final private int calcLengthOfLongestText() {
743 final StringBuilder sb = new StringBuilder();
744 if ( _ext_node_with_longest_txt_info != null ) {
745 nodeDataAsSB( _ext_node_with_longest_txt_info, sb );
746 if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) {
747 nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb );
750 return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
754 * Calculate the length of the distance between the given node and its
760 * @return the distance value
762 final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) {
763 if ( getControlPanel().isDrawPhylogram() ) {
764 if ( node.getDistanceToParent() < 0.0 ) {
767 return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() );
770 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
771 return getXdistance();
773 return getXdistance() * factor;
777 final private Color calculateColorForAnnotation( final SortedSet<Annotation> ann ) {
778 Color c = getTreeColorSet().getAnnotationColor();
779 if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
780 final StringBuilder sb = new StringBuilder();
781 for( final Annotation a : ann ) {
782 sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
784 final String ann_str = sb.toString();
785 if ( !ForesterUtil.isEmpty( ann_str ) ) {
786 c = getControlPanel().getAnnotationColors().get( ann_str );
788 c = AptxUtil.calculateColorFromString( ann_str, false );
789 getControlPanel().getAnnotationColors().put( ann_str, c );
792 c = getTreeColorSet().getAnnotationColor();
799 final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) {
800 if ( getControlPanel().isDrawPhylogram() ) {
801 if ( node.getDistanceToParent() < 0.0 ) {
804 return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() );
807 if ( ( factor == 0 ) || isNonLinedUpCladogram() ) {
808 return getOvXDistance();
810 return getOvXDistance() * factor;
814 final private void cannotOpenBrowserWarningMessage( final String type_type ) {
815 JOptionPane.showMessageDialog( this,
816 "Cannot launch web browser for " + type_type + " data of this node",
817 "Cannot launch web browser",
818 JOptionPane.WARNING_MESSAGE );
821 private void changeNodeFont( final PhylogenyNode node ) {
822 final FontChooser fc = new FontChooser();
824 if ( ( node.getNodeData().getNodeVisualData() != null ) && !node.getNodeData().getNodeVisualData().isEmpty() ) {
825 f = node.getNodeData().getNodeVisualData().getFont();
831 fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
833 List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
834 if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
835 nodes = getFoundNodesAsListOfPhylogenyNodes();
837 if ( !nodes.contains( node ) ) {
840 final int count = nodes.size();
841 String title = "Change the font for ";
846 title += ( count + " nodes" );
848 fc.showDialog( this, title );
849 if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
850 for( final PhylogenyNode n : nodes ) {
851 if ( n.getNodeData().getNodeVisualData() == null ) {
852 n.getNodeData().setNodeVisualData( new NodeVisualData() );
854 final NodeVisualData vd = n.getNodeData().getNodeVisualData();
855 final Font ff = fc.getFont();
856 vd.setFontName( ff.getFamily().trim() );
857 int s = ff.getSize();
861 if ( s > Byte.MAX_VALUE ) {
865 vd.setFontStyle( ff.getStyle() );
867 if ( _control_panel.getUseVisualStylesCb() != null ) {
868 getControlPanel().getUseVisualStylesCb().setSelected( true );
875 final private void colorizeNodes( final Color c,
876 final PhylogenyNode node,
877 final List<PhylogenyNode> additional_nodes ) {
878 _control_panel.setColorBranches( true );
879 if ( _control_panel.getUseVisualStylesCb() != null ) {
880 _control_panel.getUseVisualStylesCb().setSelected( true );
882 if ( node != null ) {
883 colorizeNodesHelper( c, node );
885 if ( additional_nodes != null ) {
886 for( final PhylogenyNode n : additional_nodes ) {
887 colorizeNodesHelper( c, n );
893 final private void colorizeSubtree( final Color c,
894 final PhylogenyNode node,
895 final List<PhylogenyNode> additional_nodes ) {
896 _control_panel.setColorBranches( true );
897 if ( _control_panel.getUseVisualStylesCb() != null ) {
898 _control_panel.getUseVisualStylesCb().setSelected( true );
900 if ( node != null ) {
901 for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
902 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
905 if ( additional_nodes != null ) {
906 for( final PhylogenyNode an : additional_nodes ) {
907 for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
908 it.next().getBranchData().setBranchColor( new BranchColor( c ) );
915 private void colorNodeFont( final PhylogenyNode node ) {
916 _color_chooser.setPreviewPanel( new JPanel() );
917 NodeColorizationActionListener al;
919 if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
920 final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
921 al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
922 count = additional_nodes.size();
923 if ( !additional_nodes.contains( node ) ) {
928 al = new NodeColorizationActionListener( _color_chooser, node );
930 String title = "Change the (node and font) color for ";
935 title += ( count + " nodes" );
937 final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null );
939 dialog.setVisible( true );
942 final private void colorSubtree( final PhylogenyNode node ) {
943 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
944 JOptionPane.showMessageDialog( this,
945 "Cannot colorize subtree in unrooted display type",
946 "Attempt to colorize subtree in unrooted display",
947 JOptionPane.WARNING_MESSAGE );
950 _color_chooser.setPreviewPanel( new JPanel() );
951 final SubtreeColorizationActionListener al;
952 final boolean color_found = getOptions().isColorAllFoundNodesWhenColoringSubtree();
953 if ( color_found && ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) ) {
954 final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
955 al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
958 al = new SubtreeColorizationActionListener( _color_chooser, node );
960 final JDialog dialog = JColorChooser.createDialog( this,
961 "Subtree colorization",
967 dialog.setVisible( true );
970 final private void copySubtree( final PhylogenyNode node ) {
971 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
972 errorMessageNoCutCopyPasteInUnrootedDisplay();
975 setNodeInPreorderToNull();
976 setCutOrCopiedTree( _phylogeny.copy( node ) );
977 final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
978 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
979 for( final PhylogenyNode n : nodes ) {
980 node_ids.add( n.getId() );
982 node_ids.add( node.getId() );
983 setCopiedAndPastedNodes( node_ids );
987 final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
988 final String tax = PhylogenyMethods.getSpecies( node );
989 String label = node.getName();
990 if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) {
991 label = label + " " + tax;
993 else if ( !ForesterUtil.isEmpty( tax ) ) {
999 if ( !ForesterUtil.isEmpty( label ) ) {
1000 label = " [" + label + "]";
1005 final private void cutSubtree( final PhylogenyNode node ) {
1006 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1007 errorMessageNoCutCopyPasteInUnrootedDisplay();
1010 if ( node.isRoot() ) {
1011 JOptionPane.showMessageDialog( this,
1012 "Cannot cut entire tree as subtree",
1013 "Attempt to cut entire tree",
1014 JOptionPane.ERROR_MESSAGE );
1017 final String label = createASimpleTextRepresentationOfANode( node );
1018 final int r = JOptionPane.showConfirmDialog( null,
1019 "Cut subtree" + label + "?",
1020 "Confirm Cutting of Subtree",
1021 JOptionPane.YES_NO_OPTION );
1022 if ( r != JOptionPane.OK_OPTION ) {
1025 setNodeInPreorderToNull();
1026 setCopiedAndPastedNodes( null );
1027 setCutOrCopiedTree( _phylogeny.copy( node ) );
1028 _phylogeny.deleteSubtree( node, true );
1029 _phylogeny.clearHashIdToNodeMap();
1030 _phylogeny.recalculateNumberOfExternalDescendants( true );
1031 resetNodeIdToDistToLeafMap();
1036 final private void cycleColors() {
1037 getMainPanel().getTreeColorSet().cycleColorScheme();
1038 for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) {
1039 tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() );
1043 final private void decreaseOvSize() {
1044 if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) {
1045 setOvMaxWidth( getOvMaxWidth() - 5 );
1046 setOvMaxHeight( getOvMaxHeight() - 5 );
1048 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1052 final private void deleteNodeOrSubtree( final PhylogenyNode node ) {
1053 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
1054 errorMessageNoCutCopyPasteInUnrootedDisplay();
1057 if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) {
1058 JOptionPane.showMessageDialog( this,
1059 "Cannot delete entire tree",
1060 "Attempt to delete entire tree",
1061 JOptionPane.ERROR_MESSAGE );
1064 final String label = createASimpleTextRepresentationOfANode( node );
1065 final Object[] options = { "Node only", "Entire subtree", "Cancel" };
1066 final int r = JOptionPane.showOptionDialog( this,
1067 "Delete" + label + "?",
1068 "Delete Node/Subtree",
1069 JOptionPane.CLOSED_OPTION,
1070 JOptionPane.QUESTION_MESSAGE,
1074 setNodeInPreorderToNull();
1075 boolean node_only = true;
1079 else if ( r != 0 ) {
1083 PhylogenyMethods.removeNode( node, _phylogeny );
1086 _phylogeny.deleteSubtree( node, true );
1088 _phylogeny.externalNodesHaveChanged();
1089 _phylogeny.clearHashIdToNodeMap();
1090 _phylogeny.recalculateNumberOfExternalDescendants( true );
1091 resetNodeIdToDistToLeafMap();
1096 final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) {
1097 makePopupMenus( node );
1098 _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node );
1099 _node_popup_menu.show( this, x, y );
1102 final private void drawArc( final double x,
1105 final double heigth,
1106 final double start_angle,
1107 final double arc_angle,
1108 final Graphics2D g ) {
1109 _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN );
1113 final private void drawLine( final double x1,
1117 final Graphics2D g ) {
1118 if ( ( x1 == x2 ) && ( y1 == y2 ) ) {
1121 _line.setLine( x1, y1, x2, y2 );
1125 final private void drawOval( final double x,
1128 final double heigth,
1129 final Graphics2D g ) {
1130 _ellipse.setFrame( x, y, width, heigth );
1134 final private void drawOvalFilled( final double x,
1137 final double heigth,
1138 final Graphics2D g ) {
1139 _ellipse.setFrame( x, y, width, heigth );
1143 final private void drawOvalGradient( final float x,
1148 final Color color_1,
1149 final Color color_2,
1150 final Color color_border ) {
1151 _ellipse.setFrame( x, y, width, heigth );
1152 g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
1154 if ( color_border != null ) {
1155 g.setPaint( color_border );
1160 final private void drawRect( final float x,
1164 final Graphics2D g ) {
1165 _rectangle.setFrame( x, y, width, heigth );
1166 g.draw( _rectangle );
1169 final private void drawRectFilled( final double x,
1172 final double heigth,
1173 final Graphics2D g ) {
1174 _rectangle.setFrame( x, y, width, heigth );
1175 g.fill( _rectangle );
1178 final private void drawRectGradient( final float x,
1183 final Color color_1,
1184 final Color color_2,
1185 final Color color_border ) {
1186 _rectangle.setFrame( x, y, width, heigth );
1187 g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
1188 g.fill( _rectangle );
1189 if ( color_border != null ) {
1190 g.setPaint( color_border );
1191 g.draw( _rectangle );
1195 private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
1196 final List<Uri> us = new ArrayList<Uri>();
1197 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
1198 for( final Uri uri : t.getUris() ) {
1203 for( final Uri uri : us ) {
1204 if ( uri != null ) {
1205 final String uri_str = uri.getValue().toString().toLowerCase();
1206 if ( getImageMap().containsKey( uri_str ) ) {
1207 final BufferedImage bi = getImageMap().get( uri_str );
1208 if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) {
1209 double scaling_factor = 1;
1210 if ( getOptions().isAllowMagnificationOfTaxonomyImages()
1211 || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) {
1212 scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight();
1214 // y = y - ( 0.9 * getYdistance() );
1215 final double hs = bi.getHeight() * scaling_factor;
1216 double ws = ( bi.getWidth() * scaling_factor ) + offset;
1217 final double my_y = y - ( 0.5 * hs );
1218 final int x_w = ( int ) ( x + ws + 0.5 );
1219 final int y_h = ( int ) ( my_y + hs + 0.5 );
1220 if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) {
1222 ( int ) ( x + 0.5 + offset ),
1223 ( int ) ( my_y + 0.5 ),
1244 final private void errorMessageNoCutCopyPasteInUnrootedDisplay() {
1245 JOptionPane.showMessageDialog( this,
1246 "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display",
1247 "Attempt to cut/copy/paste/add/delete in unrooted display",
1248 JOptionPane.ERROR_MESSAGE );
1251 private final Color getColorForFoundNode( final PhylogenyNode n ) {
1252 if ( isInCurrentExternalNodes( n ) ) {
1253 return getTreeColorSet().getFoundColor0();
1255 else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
1256 return getTreeColorSet().getFoundColor0();
1258 else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
1259 return getTreeColorSet().getFoundColor1();
1262 return getTreeColorSet().getFoundColor0and1();
1266 final private Set<Long> getCopiedAndPastedNodes() {
1267 return getMainPanel().getCopiedAndPastedNodes();
1270 final private Set<Long> getCurrentExternalNodes() {
1271 return _current_external_nodes;
1274 final private Phylogeny getCutOrCopiedTree() {
1275 return getMainPanel().getCutOrCopiedTree();
1278 private FontMetrics getFontMetricsForLargeDefaultFont() {
1279 return getTreeFontSet().getFontMetricsLarge();
1282 final private float getLastDragPointX() {
1283 return _last_drag_point_x;
1286 final private float getLastDragPointY() {
1287 return _last_drag_point_y;
1290 final private double getMaxDistanceToRoot() {
1291 if ( _max_distance_to_root < 0 ) {
1292 recalculateMaxDistanceToRoot();
1294 return _max_distance_to_root;
1297 final private float getOvMaxHeight() {
1298 return _ov_max_height;
1301 final private float getOvMaxWidth() {
1302 return _ov_max_width;
1305 final private float getOvXcorrectionFactor() {
1306 return _ov_x_correction_factor;
1309 final private float getOvXDistance() {
1310 return _ov_x_distance;
1313 final private int getOvXPosition() {
1314 return _ov_x_position;
1317 final private float getOvYDistance() {
1318 return _ov_y_distance;
1321 final private int getOvYPosition() {
1322 return _ov_y_position;
1325 final private int getOvYStart() {
1329 final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
1330 final List<Accession> pdb_ids = new ArrayList<Accession>();
1331 if ( node.getNodeData().isHasSequence() ) {
1332 final Sequence seq = node.getNodeData().getSequence();
1333 if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
1334 final SortedSet<Accession> cross_refs = seq.getCrossReferences();
1335 for( final Accession acc : cross_refs ) {
1336 if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
1345 final private double getScaleDistance() {
1346 return _scale_distance;
1349 final private String getScaleLabel() {
1350 return _scale_label;
1353 final private TreeFontSet getTreeFontSet() {
1354 return getMainPanel().getTreeFontSet();
1357 final private float getUrtFactor() {
1361 final private float getUrtFactorOv() {
1362 return _urt_factor_ov;
1365 final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) {
1368 showNodeFrame( node );
1383 colorSubtree( node );
1385 case COLOR_NODE_FONT:
1386 colorNodeFont( node );
1388 case CHANGE_NODE_FONT:
1389 changeNodeFont( node );
1407 copySubtree( node );
1410 pasteSubtree( node );
1412 case DELETE_NODE_OR_SUBTREE:
1413 deleteNodeOrSubtree( node );
1416 addEmptyNode( node );
1418 case EDIT_NODE_DATA:
1419 showNodeEditFrame( node );
1424 case SORT_DESCENDENTS:
1425 sortDescendants( node );
1427 case GET_EXT_DESC_DATA:
1428 showExtDescNodeData( node, '_' );
1430 case UNCOLLAPSE_ALL:
1431 uncollapseAll( node );
1434 orderSubtree( node );
1437 throw new IllegalArgumentException( "unknown action: " + action );
1441 final private void increaseCurrentExternalNodesDataBufferChangeCounter() {
1442 _current_external_nodes_data_buffer_change_counter++;
1445 final private void increaseOvSize() {
1446 if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth()
1448 && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect()
1449 .getHeight() / 2 ) ) ) {
1450 setOvMaxWidth( getOvMaxWidth() + 5 );
1451 setOvMaxHeight( getOvMaxHeight() + 5 );
1453 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1457 final private void init() {
1458 _color_chooser = new JColorChooser();
1459 _rollover_popup = new JTextArea();
1460 _rollover_popup.setFont( POPUP_FONT );
1461 resetNodeIdToDistToLeafMap();
1463 setTreeFile( null );
1465 initializeOvSettings();
1466 resetDepthCollapseDepthValue();
1467 resetRankCollapseRankValue();
1468 setStartingAngle( ( TWO_PI * 3 ) / 4 );
1469 final ImageLoader il = new ImageLoader( this );
1470 new Thread( il ).start();
1473 final private void initializeOvSettings() {
1474 setOvMaxHeight( getConfiguration().getOvMaxHeight() );
1475 setOvMaxWidth( getConfiguration().getOvMaxWidth() );
1478 final private boolean inOvVirtualRectangle( final int x, final int y ) {
1479 return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
1480 && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
1481 && ( y >= ( getOvVirtualRectangle().y - 1 ) )
1482 && ( y <= ( getOvVirtualRectangle().y + getOvVirtualRectangle().height + 1 ) ) );
1485 final private boolean inOvVirtualRectangle( final MouseEvent e ) {
1486 return ( inOvVirtualRectangle( e.getX(), e.getY() ) );
1489 final private boolean isCanBlast( final PhylogenyNode node ) {
1490 if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) {
1493 return Blast.isContainsQueryForBlast( node );
1496 final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
1497 final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
1499 return a.getValue();
1504 final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
1505 if ( node.getNodeData().isHasTaxonomy() && ( ( !ForesterUtil
1506 .isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
1507 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
1508 || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) )
1509 || ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
1510 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
1518 final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) {
1519 return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
1522 private boolean isInFoundNodes( final PhylogenyNode n ) {
1523 return isInFoundNodes0( n ) || isInFoundNodes1( n );
1526 final private boolean isInFoundNodes0( final PhylogenyNode node ) {
1527 return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
1530 final private boolean isInFoundNodes1( final PhylogenyNode node ) {
1531 return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
1534 final private boolean isInOv() {
1538 final private boolean isNodeDataInvisible( final PhylogenyNode node ) {
1540 if ( getControlPanel().isShowTaxonomyImages() ) {
1541 y_dist = 40 + ( int ) getYdistance();
1543 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
1544 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) )
1545 || ( ( node.getParent() != null ) && ( node.getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
1548 final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
1549 return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
1550 || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
1551 || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) )
1552 || ( node.getXcoord() > ( getVisibleRect().getMaxX() + 20 ) ) );
1555 final private boolean isNonLinedUpCladogram() {
1556 return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP;
1559 final private void keyPressedCalls( final KeyEvent e ) {
1560 if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) {
1561 if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) {
1562 if ( !isInOvRect() ) {
1563 setInOvRect( true );
1566 else if ( isInOvRect() ) {
1567 setInOvRect( false );
1570 if ( e.isAltDown() ) {
1571 if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME )
1572 || ( e.getKeyCode() == KeyEvent.VK_C ) || ( e.getKeyCode() == KeyEvent.VK_BACK_SPACE ) ) {
1573 getControlPanel().showWhole();
1575 else if ( e.isShiftDown()
1576 && ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) ) {
1577 getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
1578 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1580 else if ( e.isShiftDown() && plusPressed( e.getKeyCode() ) ) {
1581 getMainPanel().getTreeFontSet().increaseFontSize();
1582 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1584 else if ( e.getKeyCode() == KeyEvent.VK_O ) {
1585 getControlPanel().orderPressed( this );
1587 else if ( e.getKeyCode() == KeyEvent.VK_R ) {
1588 getControlPanel().returnedToSuperTreePressed();
1590 else if ( e.getKeyCode() == KeyEvent.VK_U ) {
1591 getControlPanel().uncollapseAll( this );
1592 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1594 else if ( e.getKeyCode() == KeyEvent.VK_UP ) {
1595 getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
1596 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1598 else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1599 getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
1600 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1602 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1603 getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
1604 AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1605 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1607 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1608 getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
1609 AptxConstants.WHEEL_ZOOM_IN_FACTOR );
1610 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1612 else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) {
1613 getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR );
1614 getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR,
1615 AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR );
1616 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1618 else if ( plusPressed( e.getKeyCode() ) ) {
1619 getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR,
1620 AptxConstants.WHEEL_ZOOM_IN_FACTOR );
1621 getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR );
1622 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false );
1626 if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN )
1627 || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) {
1631 if ( e.getKeyCode() == KeyEvent.VK_DOWN ) {
1634 else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) {
1638 else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) {
1642 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
1643 scroll_position.x = scroll_position.x + dx;
1644 scroll_position.y = scroll_position.y + dy;
1645 if ( scroll_position.x <= 0 ) {
1646 scroll_position.x = 0;
1649 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
1650 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
1651 if ( scroll_position.x >= max_x ) {
1652 scroll_position.x = max_x;
1655 if ( scroll_position.y <= 0 ) {
1656 scroll_position.y = 0;
1659 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
1660 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
1661 if ( scroll_position.y >= max_y ) {
1662 scroll_position.y = max_y;
1666 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
1668 else if ( e.getKeyCode() == KeyEvent.VK_S ) {
1669 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1670 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1671 setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT );
1672 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1675 else if ( e.getKeyCode() == KeyEvent.VK_A ) {
1676 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
1677 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
1678 setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT );
1679 if ( getStartingAngle() < 0 ) {
1680 setStartingAngle( TWO_PI + getStartingAngle() );
1682 getControlPanel().displayedPhylogenyMightHaveChanged( false );
1685 else if ( e.getKeyCode() == KeyEvent.VK_D ) {
1686 boolean selected = false;
1687 if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) {
1688 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL );
1692 getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
1694 getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected );
1697 else if ( e.getKeyCode() == KeyEvent.VK_X ) {
1698 switchDisplaygetPhylogenyGraphicsType();
1701 else if ( e.getKeyCode() == KeyEvent.VK_C ) {
1705 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) {
1706 MainFrame.cycleOverview( getOptions(), this );
1709 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) {
1712 else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) {
1716 if ( e.getKeyCode() == KeyEvent.VK_HOME || e.getKeyCode() == KeyEvent.VK_ESCAPE ) {
1717 getControlPanel().showWhole();
1719 else if ( e.getKeyCode() == KeyEvent.VK_PAGE_UP ) {
1720 getMainPanel().getTreeFontSet().increaseFontSize();
1721 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1723 else if ( e.getKeyCode() == KeyEvent.VK_PAGE_DOWN ) {
1724 getMainPanel().getTreeFontSet().decreaseFontSize( 1, false );
1725 getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true );
1730 final private void makePopupMenus( final PhylogenyNode node ) {
1731 _node_popup_menu = new JPopupMenu();
1732 final List<String> clickto_names = _main_panel.getControlPanel().getSingleClickToNames();
1733 _node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
1734 for( int i = 0; i < clickto_names.size(); i++ ) {
1735 final String title = clickto_names.get( i );
1736 _node_popup_menu_items[ i ] = new JMenuItem( title );
1737 if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
1738 final String id = isCanOpenSeqWeb( node );
1739 if ( !ForesterUtil.isEmpty( id ) ) {
1740 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
1741 _node_popup_menu_items[ i ].setEnabled( true );
1744 _node_popup_menu_items[ i ].setEnabled( false );
1747 else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
1748 final List<Accession> accs = getPdbAccs( node );
1749 _node_popup_menu_items[ i ] = new JMenuItem( title );
1750 if ( !ForesterUtil.isEmpty( accs ) ) {
1751 if ( accs.size() == 1 ) {
1752 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
1753 + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
1754 _node_popup_menu_items[ i ].setEnabled( true );
1756 else if ( accs.size() == 2 ) {
1757 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
1758 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
1759 + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
1760 _node_popup_menu_items[ i ].setEnabled( true );
1762 else if ( accs.size() == 3 ) {
1763 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
1764 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
1765 + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
1766 + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
1767 _node_popup_menu_items[ i ].setEnabled( true );
1770 _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
1771 + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
1772 + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
1773 + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
1774 _node_popup_menu_items[ i ].setEnabled( true );
1778 _node_popup_menu_items[ i ].setEnabled( false );
1781 else if ( title.startsWith( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] ) ) {
1782 _node_popup_menu_items[ i ]
1783 .setText( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] + ": "
1784 + getOptions().getExtDescNodeDataToReturn().toString() );
1786 else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
1787 _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
1789 else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) {
1790 _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
1792 else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
1793 if ( !getOptions().isEditable() ) {
1796 _node_popup_menu_items[ i ].setEnabled( isCanDelete() );
1798 else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) {
1799 if ( !getOptions().isEditable() ) {
1802 _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) );
1804 else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) {
1805 if ( !getOptions().isEditable() ) {
1808 _node_popup_menu_items[ i ].setEnabled( isCanCopy() );
1810 else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) {
1811 if ( !getOptions().isEditable() ) {
1814 _node_popup_menu_items[ i ].setEnabled( isCanPaste() );
1816 else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) {
1817 if ( !getOptions().isEditable() ) {
1821 else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) {
1822 if ( !getOptions().isEditable() ) {
1826 else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) {
1827 _node_popup_menu_items[ i ].setEnabled( isCanReroot() );
1829 else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) {
1830 _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) );
1832 else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) {
1833 _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() );
1835 else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) {
1836 _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) );
1838 else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) {
1839 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 );
1841 else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
1842 _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
1844 else if ( title.equals( Configuration.clickto_options[ Configuration.uncollapse_all ][ 0 ] ) ) {
1845 _node_popup_menu_items[ i ].setEnabled( isCanUncollapseAll( node ) );
1847 _node_popup_menu_items[ i ].addActionListener( this );
1848 _node_popup_menu.add( _node_popup_menu_items[ i ] );
1852 private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
1853 if ( node != null ) {
1854 if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) {
1855 if ( sb.length() > 0 ) {
1858 sb.append( node.getName() );
1860 if ( node.getNodeData().isHasSequence() ) {
1861 if ( getControlPanel().isShowSeqSymbols()
1862 && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
1863 if ( sb.length() > 0 ) {
1866 sb.append( node.getNodeData().getSequence().getSymbol() );
1868 if ( getControlPanel().isShowGeneNames()
1869 && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
1870 if ( sb.length() > 0 ) {
1873 sb.append( node.getNodeData().getSequence().getGeneName() );
1875 if ( getControlPanel().isShowSeqNames()
1876 && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
1877 if ( sb.length() > 0 ) {
1880 sb.append( node.getNodeData().getSequence().getName() );
1882 if ( getControlPanel().isShowSequenceAcc()
1883 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
1884 if ( sb.length() > 0 ) {
1887 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
1888 sb.append( node.getNodeData().getSequence().getAccession().getSource() );
1891 sb.append( node.getNodeData().getSequence().getAccession().getValue() );
1894 if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
1895 if ( sb.length() > 0 ) {
1898 sb.append( propertiesToString( node ) );
1903 private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
1904 if ( _control_panel.isShowTaxonomyRank() && !ForesterUtil.isEmpty( taxonomy.getRank() ) ) {
1906 sb.append( taxonomy.getRank() );
1909 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
1910 sb.append( taxonomy.getTaxonomyCode() );
1913 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
1914 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
1915 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
1916 if ( getOptions().isAbbreviateScientificTaxonNames()
1917 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
1918 abbreviateScientificName( taxonomy.getScientificName(), sb );
1921 sb.append( taxonomy.getScientificName() );
1924 sb.append( taxonomy.getCommonName() );
1927 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
1928 if ( getOptions().isAbbreviateScientificTaxonNames()
1929 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
1930 abbreviateScientificName( taxonomy.getScientificName(), sb );
1933 sb.append( taxonomy.getScientificName() );
1937 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
1938 sb.append( taxonomy.getCommonName() );
1942 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
1943 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
1944 if ( getOptions().isAbbreviateScientificTaxonNames()
1945 && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
1946 abbreviateScientificName( taxonomy.getScientificName(), sb );
1949 sb.append( taxonomy.getScientificName() );
1954 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
1955 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
1956 sb.append( taxonomy.getCommonName() );
1962 private final String obtainTitleForExtDescNodeData() {
1963 return getOptions().getExtDescNodeDataToReturn().toString();
1966 final private void openPdbWeb( final PhylogenyNode node ) {
1967 final List<Accession> pdb_ids = getPdbAccs( node );
1968 if ( ForesterUtil.isEmpty( pdb_ids ) ) {
1969 cannotOpenBrowserWarningMessage( "PDB" );
1972 final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
1973 if ( !ForesterUtil.isEmpty( uri_strs ) ) {
1974 for( final String uri_str : uri_strs ) {
1976 AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" );
1978 catch ( final IOException e ) {
1979 AptxUtil.showErrorMessage( this, e.toString() );
1980 e.printStackTrace();
1982 catch ( final URISyntaxException e ) {
1983 AptxUtil.showErrorMessage( this, e.toString() );
1984 e.printStackTrace();
1989 cannotOpenBrowserWarningMessage( "PDB" );
1993 final private void openSeqWeb( final PhylogenyNode node ) {
1994 if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
1995 cannotOpenBrowserWarningMessage( "sequence" );
1998 final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
1999 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2001 AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" );
2003 catch ( final IOException e ) {
2004 AptxUtil.showErrorMessage( this, e.toString() );
2005 e.printStackTrace();
2007 catch ( final URISyntaxException e ) {
2008 AptxUtil.showErrorMessage( this, e.toString() );
2009 e.printStackTrace();
2013 cannotOpenBrowserWarningMessage( "sequence" );
2017 final private void openTaxWeb( final PhylogenyNode node ) {
2018 if ( !isCanOpenTaxWeb( node ) ) {
2019 cannotOpenBrowserWarningMessage( "taxonomic" );
2022 String uri_str = null;
2023 final Taxonomy tax = node.getNodeData().getTaxonomy();
2024 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
2025 && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
2027 uri_str = new URI( tax.getIdentifier().getValue() ).toString();
2029 catch ( final URISyntaxException e ) {
2030 AptxUtil.showErrorMessage( this, e.toString() );
2032 e.printStackTrace();
2035 else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
2036 && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
2037 && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" )
2038 || tax.getIdentifier().getProvider().equalsIgnoreCase( "uniprot" ) ) ) {
2040 uri_str = "http://www.uniprot.org/taxonomy/"
2041 + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF_8 );
2043 catch ( final UnsupportedEncodingException e ) {
2044 AptxUtil.showErrorMessage( this, e.toString() );
2045 e.printStackTrace();
2048 else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
2050 uri_str = "http://www.uniprot.org/taxonomy/?query="
2051 + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF_8 );
2053 catch ( final UnsupportedEncodingException e ) {
2054 AptxUtil.showErrorMessage( this, e.toString() );
2055 e.printStackTrace();
2058 else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
2060 uri_str = "http://www.uniprot.org/taxonomy/?query="
2061 + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF_8 );
2063 catch ( final UnsupportedEncodingException e ) {
2064 AptxUtil.showErrorMessage( this, e.toString() );
2065 e.printStackTrace();
2068 else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
2070 uri_str = "http://www.uniprot.org/taxonomy/?query="
2071 + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF_8 );
2073 catch ( final UnsupportedEncodingException e ) {
2074 AptxUtil.showErrorMessage( this, e.toString() );
2075 e.printStackTrace();
2078 if ( !ForesterUtil.isEmpty( uri_str ) ) {
2080 AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_tax" );
2082 catch ( final IOException e ) {
2083 AptxUtil.showErrorMessage( this, e.toString() );
2084 e.printStackTrace();
2086 catch ( final URISyntaxException e ) {
2087 AptxUtil.showErrorMessage( this, e.toString() );
2088 e.printStackTrace();
2092 cannotOpenBrowserWarningMessage( "taxonomic" );
2096 final private void paintBranchLength( final Graphics2D g,
2097 final PhylogenyNode node,
2098 final boolean to_pdf,
2099 final boolean to_graphics_file ) {
2100 g.setFont( getTreeFontSet().getSmallFont() );
2101 if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) {
2102 g.setColor( Color.BLACK );
2105 g.setColor( getTreeColorSet().getBranchLengthColor() );
2107 if ( !node.isRoot() ) {
2108 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2109 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
2110 node.getParent().getXcoord() + EURO_D,
2111 node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
2114 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2115 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
2116 node.getParent().getXcoord() + ROUNDED_D,
2117 node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
2121 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
2122 node.getParent().getXcoord() + 3,
2123 node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
2128 TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ),
2130 node.getYcoord() - getTreeFontSet().getSmallMaxDescent(),
2135 final private void paintBranchLite( final Graphics2D g,
2140 final PhylogenyNode node ) {
2141 g.setColor( getTreeColorSet().getOvColor() );
2142 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
2143 drawLine( x1, y1, x2, y2, g );
2145 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
2146 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
2147 ( g ).draw( _quad_curve );
2149 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
2150 final float dx = x2 - x1;
2151 final float dy = y2 - y1;
2152 _cubic_curve.setCurve( x1,
2160 ( g ).draw( _cubic_curve );
2163 final float x2a = x2;
2164 final float x1a = x1;
2165 // draw the vertical line
2166 if ( node.isFirstChildNode() || node.isLastChildNode() ) {
2167 drawLine( x1, y1, x1, y2, g );
2169 // draw the horizontal line
2170 drawLine( x1a, y2, x2a, y2, g );
2175 * Paint a branch which consists of a vertical and a horizontal bar
2176 * @param is_ind_found_nodes
2178 final private void paintBranchRectangular( final Graphics2D g,
2183 final PhylogenyNode node,
2184 final boolean to_pdf,
2185 final boolean to_graphics_file ) {
2186 assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file );
2187 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) {
2188 drawLine( x1, y1, x2, y2, g );
2190 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) {
2191 _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 );
2192 g.draw( _quad_curve );
2194 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) {
2195 final float dx = x2 - x1;
2196 final float dy = y2 - y1;
2197 _cubic_curve.setCurve( x1,
2205 g.draw( _cubic_curve );
2208 final float x2a = x2;
2209 final float x1a = x1;
2211 if ( node.isFirstChildNode() || node.isLastChildNode()
2212 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
2213 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2214 if ( !to_graphics_file && !to_pdf
2215 && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) )
2216 && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) )
2217 || ( ( y2 > ( getVisibleRect().getMaxY() + 20 ) )
2218 && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) {
2222 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2223 float x2c = x1 + EURO_D;
2227 drawLine( x1, y1, x2c, y2, g );
2229 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2231 y2_r = y2 - ROUNDED_D;
2235 drawLine( x1, y1, x1, y2_r, g );
2238 y2_r = y2 + ROUNDED_D;
2242 drawLine( x1, y1, x1, y2_r, g );
2246 drawLine( x1, y1, x1, y2, g );
2250 // draw the horizontal line
2251 if ( !to_graphics_file && !to_pdf && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) )
2252 || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) {
2256 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
2257 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2258 x1_r = x1a + ROUNDED_D;
2260 drawLine( x1_r, y2, x2a, y2, g );
2263 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2264 final float x1c = x1a + EURO_D;
2266 drawLine( x1c, y2, x2a, y2, g );
2270 drawLine( x1a, y2, x2a, y2, g );
2274 final double w = PhylogenyMethods.getBranchWidthValue( node );
2275 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2276 x1_r = x1a + ROUNDED_D;
2278 drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
2281 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2282 final float x1c = x1a + EURO_D;
2284 drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
2288 drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
2291 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2296 final double diff = y2 - y2_r;
2297 _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN );
2300 _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN );
2305 if ( node.isExternal() ) {
2306 paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
2310 final private double paintCirculars( final PhylogenyNode n,
2311 final Phylogeny phy,
2312 final float center_x,
2313 final float center_y,
2314 final double radius,
2315 final boolean radial_labels,
2317 final boolean to_pdf,
2318 final boolean to_graphics_file ) {
2319 if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
2320 if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
2321 System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
2323 return _urt_nodeid_angle_map.get( n.getId() );
2326 final List<PhylogenyNode> descs = n.getDescendants();
2328 for( final PhylogenyNode desc : descs ) {
2329 sum += paintCirculars( desc,
2340 if ( !n.isRoot() ) {
2341 r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
2343 final double theta = sum / descs.size();
2344 n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) );
2345 n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) );
2346 _urt_nodeid_angle_map.put( n.getId(), theta );
2347 for( final PhylogenyNode desc : descs ) {
2348 paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file );
2354 final private void paintCircularsLite( final PhylogenyNode n,
2355 final Phylogeny phy,
2359 final Graphics2D g ) {
2360 if ( n.isExternal() ) {
2364 final List<PhylogenyNode> descs = n.getDescendants();
2365 for( final PhylogenyNode desc : descs ) {
2366 paintCircularsLite( desc, phy, center_x, center_y, radius, g );
2369 if ( !n.isRoot() ) {
2370 r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth );
2372 final double theta = _urt_nodeid_angle_map.get( n.getId() );
2373 n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) );
2374 n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) );
2375 for( final PhylogenyNode desc : descs ) {
2376 paintBranchCircularLite( n, desc, g );
2381 final private void paintCollapsedNode( final Graphics2D g,
2382 final PhylogenyNode node,
2383 final boolean to_graphics_file,
2384 final boolean to_pdf,
2385 final boolean is_in_found_nodes ) {
2391 if ( _found_nodes_0 != null || _found_nodes_1 != null ) {
2392 res = calcFoundNodesInSubtree( node );
2394 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2399 // else if ( is_in_found_nodes ) {
2400 // c = getColorForFoundNode( node );
2402 // else if ( getControlPanel().isColorAccordingToSequence() ) {
2403 // c = getSequenceBasedColor( node );
2405 // else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
2406 // c = getTaxonomyBasedColor( node );
2408 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
2409 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
2410 c = PhylogenyMethods.getBranchColorValue( node );
2412 else if ( to_pdf ) {
2413 g.setColor( getTreeColorSet().getBranchColorForPdf() );
2416 c = getTreeColorSet().getCollapseFillColor();
2418 double d = node.getAllExternalDescendants().size();
2421 if ( getControlPanel().isDrawPhylogram() ) {
2423 d = 0.75 * _y_distance;
2426 d = 0.25 * Math.log10( d ) * _y_distance;
2428 final float half_box_size = 0.5f * getOptions().getDefaultNodeShapeSize();
2429 if ( d < half_box_size ) {
2433 final float xx = node.getXcoord() - ( getOptions().getDefaultNodeShapeSize() );
2434 xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
2435 _polygon.moveTo( xxx, node.getYcoord() + 0.5 );
2436 _polygon.lineTo( xxx, node.getYcoord() - 0.5 );
2437 s = _options.isCollapsedWithAverageHeigh()
2438 ? PhylogenyMethods.calculateAverageTreeHeight( node ) * _x_correction_factor : 1;
2439 _polygon.lineTo( node.getXcoord() + s, node.getYcoord() - d );
2440 _polygon.lineTo( node.getXcoord() + s, node.getYcoord() + d );
2441 _polygon.closePath();
2448 d = ( Math.log10( d ) * _y_distance ) / 2.5;
2450 final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
2451 if ( d < box_size ) {
2454 final float xx = node.getXcoord() - ( 2 * box_size );
2455 xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1;
2457 _polygon.moveTo( xxx, node.getYcoord() );
2458 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
2459 _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
2460 _polygon.closePath();
2462 if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
2466 else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
2467 g.setColor( getBackground() );
2472 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
2473 g.setPaint( new GradientPaint( xxx,
2477 ( float ) ( node.getYcoord() - d ),
2484 paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes, s );
2487 final private void paintConfidenceValues( final Graphics2D g,
2488 final PhylogenyNode node,
2489 final boolean to_pdf,
2490 final boolean to_graphics_file ) {
2491 final List<Confidence> confidences = node.getBranchData().getConfidences();
2492 boolean not_first = false;
2493 Collections.sort( confidences );
2494 final StringBuilder sb = new StringBuilder();
2495 for( final Confidence confidence : confidences ) {
2496 if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE ) || ( !ForesterUtil.isEmpty( confidence.getType() )
2497 && confidence.getType().equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) {
2498 final double value = confidence.getValue();
2499 if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
2500 if ( value < getOptions().getMinConfidenceValue() ) {
2509 sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil
2510 .round( value, getOptions().getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
2511 if ( getOptions().isShowConfidenceStddev() ) {
2512 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
2514 sb.append( FORMATTER_CONFIDENCE
2515 .format( ForesterUtil.round( confidence.getStandardDeviation(),
2517 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
2524 if ( sb.length() > 0 ) {
2525 final float parent_x = node.getParent().getXcoord();
2526 float x = node.getXcoord();
2527 g.setFont( getTreeFontSet().getSmallFont() );
2528 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
2531 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
2534 if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) {
2535 g.setColor( Color.BLACK );
2538 g.setColor( getTreeColorSet().getConfidenceColor() );
2540 final String conf_str = sb.toString();
2541 TreePanel.drawString( conf_str,
2542 parent_x + ( ( x - parent_x
2543 - getTreeFontSet().getFontMetricsSmall().stringWidth( conf_str ) ) / 2 ),
2544 ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
2549 final private void paintGainedAndLostCharacters( final Graphics2D g,
2550 final PhylogenyNode node,
2551 final String gained,
2552 final String lost ) {
2553 if ( node.getParent() != null ) {
2554 final float parent_x = node.getParent().getXcoord();
2555 final float x = node.getXcoord();
2556 g.setFont( getTreeFontSet().getLargeFont() );
2557 g.setColor( getTreeColorSet().getGainedCharactersColor() );
2558 if ( AptxConstants.SPECIAL_CUSTOM ) {
2559 g.setColor( Color.BLUE );
2561 TreePanel.drawString( gained,
2562 parent_x + ( ( x - parent_x
2563 - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
2564 ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
2566 g.setColor( getTreeColorSet().getLostCharactersColor() );
2569 parent_x + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) )
2571 ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
2576 private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) {
2577 final RenderableMsaSequence rs = RenderableMsaSequence
2578 .createInstance( node.getNodeData().getSequence().getMolecularSequence(),
2579 node.getNodeData().getSequence().getType(),
2580 getConfiguration() );
2582 final int default_height = 8;
2583 final float y = getYdistance();
2584 final int h = ( y / 2 ) < default_height ? ForesterUtil.roundToInt( y * 2 ) : default_height;
2585 rs.setRenderingHeight( h > 1 ? h : 1 );
2586 if ( getControlPanel().isDrawPhylogram() ) {
2587 rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
2588 node.getYcoord() - ( h / 2.0f ),
2594 rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
2595 node.getYcoord() - ( h / 2.0f ),
2604 * Draw a box at the indicated node.
2611 final private void paintNodeBox( final float x,
2613 final PhylogenyNode node,
2615 final boolean to_pdf,
2616 final boolean to_graphics_file ) {
2617 if ( node.isCollapse() ) {
2620 // if this node should be highlighted, do so
2621 if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
2622 g.setColor( getTreeColorSet().getFoundColor0() );
2623 drawOval( x - 8, y - 8, 16, 16, g );
2624 drawOval( x - 9, y - 8, 17, 17, g );
2625 drawOval( x - 9, y - 9, 18, 18, g );
2627 if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
2628 || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
2629 || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
2630 || ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
2631 && ( node.getNodeData().getNodeVisualData() != null )
2632 && ( !node.getNodeData().getNodeVisualData().isEmpty() ) )
2633 || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null )
2634 && ( ( node.getNodeData().getNodeVisualData().getNodeColor() != null )
2635 || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
2636 || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT )
2637 || ( node.getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
2638 || ( getControlPanel().isEvents() && node.isHasAssignedEvent()
2639 && ( node.getNodeData().getEvent().isDuplication()
2640 || node.getNodeData().getEvent().isSpeciation()
2641 || node.getNodeData().getEvent().isSpeciationOrDuplication() ) ) ) {
2642 NodeVisualData vis = null;
2643 if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
2644 && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) {
2645 vis = node.getNodeData().getNodeVisualData();
2647 float box_size = getOptions().getDefaultNodeShapeSize();
2648 if ( ( vis != null ) && ( vis.getSize() != NodeVisualData.DEFAULT_SIZE ) ) {
2649 box_size = vis.getSize();
2651 final float half_box_size = box_size / 2.0f;
2652 Color outline_color = null;
2653 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2654 outline_color = Color.BLACK;
2656 else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
2657 outline_color = getColorForFoundNode( node );
2659 else if ( vis != null ) {
2660 if ( vis.getNodeColor() != null ) {
2661 outline_color = vis.getNodeColor();
2663 else if ( vis.getFontColor() != null ) {
2664 outline_color = vis.getFontColor();
2667 else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
2668 final Event event = node.getNodeData().getEvent();
2669 if ( event.isDuplication() ) {
2670 outline_color = getTreeColorSet().getDuplicationBoxColor();
2672 else if ( event.isSpeciation() ) {
2673 outline_color = getTreeColorSet().getSpecBoxColor();
2675 else if ( event.isSpeciationOrDuplication() ) {
2676 outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
2679 if ( outline_color == null ) {
2680 outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
2681 if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
2682 outline_color = getTreeColorSet().getBranchColorForPdf();
2685 NodeShape shape = null;
2686 if ( vis != null ) {
2687 if ( vis.getShape() == NodeShape.CIRCLE ) {
2688 shape = NodeShape.CIRCLE;
2690 else if ( vis.getShape() == NodeShape.RECTANGLE ) {
2691 shape = NodeShape.RECTANGLE;
2694 if ( shape == null ) {
2695 if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
2696 shape = NodeShape.CIRCLE;
2698 else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) {
2699 shape = NodeShape.RECTANGLE;
2702 NodeFill fill = null;
2703 if ( vis != null ) {
2704 if ( vis.getFillType() == NodeFill.SOLID ) {
2705 fill = NodeFill.SOLID;
2707 else if ( vis.getFillType() == NodeFill.NONE ) {
2708 fill = NodeFill.NONE;
2710 else if ( vis.getFillType() == NodeFill.GRADIENT ) {
2711 fill = NodeFill.GRADIENT;
2714 if ( fill == null ) {
2715 if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
2716 fill = NodeFill.SOLID;
2718 else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
2719 fill = NodeFill.NONE;
2721 else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
2722 fill = NodeFill.GRADIENT;
2725 Color vis_fill_color = null;
2726 if ( ( vis != null ) && ( vis.getNodeColor() != null ) ) {
2727 vis_fill_color = vis.getNodeColor();
2729 if ( shape == NodeShape.CIRCLE ) {
2730 if ( fill == NodeFill.GRADIENT ) {
2731 drawOvalGradient( x - half_box_size,
2736 to_pdf ? Color.WHITE : outline_color,
2737 to_pdf ? outline_color : getBackground(),
2740 else if ( fill == NodeFill.NONE ) {
2741 Color background = getBackground();
2743 background = Color.WHITE;
2745 drawOvalGradient( x - half_box_size,
2754 else if ( fill == NodeVisualData.NodeFill.SOLID ) {
2755 if ( vis_fill_color != null ) {
2756 g.setColor( vis_fill_color );
2759 g.setColor( outline_color );
2761 drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
2764 else if ( shape == NodeVisualData.NodeShape.RECTANGLE ) {
2765 if ( fill == NodeVisualData.NodeFill.GRADIENT ) {
2766 drawRectGradient( x - half_box_size,
2771 to_pdf ? Color.WHITE : outline_color,
2772 to_pdf ? outline_color : getBackground(),
2775 else if ( fill == NodeVisualData.NodeFill.NONE ) {
2776 Color background = getBackground();
2778 background = Color.WHITE;
2780 drawRectGradient( x - half_box_size,
2789 else if ( fill == NodeVisualData.NodeFill.SOLID ) {
2790 if ( vis_fill_color != null ) {
2791 g.setColor( vis_fill_color );
2794 g.setColor( outline_color );
2796 drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
2802 final private int paintNodeData( final Graphics2D g,
2803 final PhylogenyNode node,
2804 final boolean to_graphics_file,
2805 final boolean to_pdf,
2806 final boolean is_in_found_nodes,
2807 final double add ) {
2808 if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
2811 if ( getControlPanel().isWriteBranchLengthValues()
2812 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
2813 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
2814 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
2815 && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
2816 paintBranchLength( g, node, to_pdf, to_graphics_file );
2818 if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
2821 if ( !getControlPanel().isShowExternalData() && ( node.isExternal() || node.isCollapse() ) ) {
2829 final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
2830 if ( getControlPanel().isShowTaxonomyImages() && ( getImageMap() != null ) && !getImageMap().isEmpty()
2831 && node.getNodeData().isHasTaxonomy() && ( ( node.getNodeData().getTaxonomy().getUris() != null )
2832 && !node.getNodeData().getTaxonomy().getUris().isEmpty() ) ) {
2833 x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
2835 if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
2836 || getControlPanel().isShowTaxonomyCommonNames() || getControlPanel().isShowTaxonomyRank() )
2837 && node.getNodeData().isHasTaxonomy() ) {
2838 x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
2840 setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
2841 final boolean saw_species = _sb.length() > 0;
2843 nodeDataAsSB( node, _sb );
2844 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
2845 if ( ( _sb.length() == 0 ) && !saw_species ) {
2846 if ( getOptions().isShowAbbreviatedLabelsForCollapsedNodes()
2847 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
2848 || getControlPanel().isShowSeqNames() || getControlPanel().isShowNodeNames() ) ) {
2849 final PhylogenyNode first = PhylogenyMethods.getFirstExternalNode( node );
2850 final PhylogenyNode last = PhylogenyMethods.getLastExternalNode( node );
2851 if ( getControlPanel().isShowTaxonomyCode() && first.getNodeData().isHasTaxonomy()
2852 && last.getNodeData().isHasTaxonomy()
2853 && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getTaxonomyCode() )
2854 && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
2855 addLabelForCollapsed( first.getNodeData().getTaxonomy().getTaxonomyCode(),
2856 last.getNodeData().getTaxonomy().getTaxonomyCode(),
2857 node.getAllExternalDescendants().size(),
2860 else if ( getControlPanel().isShowTaxonomyScientificNames() && first.getNodeData().isHasTaxonomy()
2861 && last.getNodeData().isHasTaxonomy()
2862 && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getScientificName() )
2863 && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getScientificName() ) ) {
2864 addLabelForCollapsed( first.getNodeData().getTaxonomy().getScientificName(),
2865 last.getNodeData().getTaxonomy().getScientificName(),
2866 node.getAllExternalDescendants().size(),
2869 else if ( getControlPanel().isShowSeqNames() && first.getNodeData().isHasSequence()
2870 && last.getNodeData().isHasSequence()
2871 && !ForesterUtil.isEmpty( first.getNodeData().getSequence().getName() )
2872 && !ForesterUtil.isEmpty( last.getNodeData().getSequence().getName() ) ) {
2873 addLabelForCollapsed( first.getNodeData().getSequence().getName(),
2874 last.getNodeData().getSequence().getName(),
2875 node.getAllExternalDescendants().size(),
2878 else if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( first.getName() )
2879 && !ForesterUtil.isEmpty( last.getName() ) ) {
2880 addLabelForCollapsed( first.getName(),
2882 node.getAllExternalDescendants().size(),
2887 else if ( ( _sb.length() > 0 ) || saw_species ) {
2888 // _sb.setLength( 0 );
2890 _sb.append( node.getAllExternalDescendants().size() );
2892 if ( _found_nodes_0 != null || _found_nodes_1 != null ) {
2893 int[] res = calcFoundNodesInSubtree( node );
2894 if ( res[ 0 ] > 0 ) {
2896 _sb.append( res[ 0 ] );
2898 _sb.append( res[ 1 ] );
2905 // _sb.setLength( 0 );
2907 // nodeDataAsSB( node, _sb );
2908 final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
2909 float down_shift_factor = 3.0f;
2910 if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
2911 down_shift_factor = 1;
2914 if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM
2915 && ( node.isExternal() || node.isCollapse() ) ) {
2916 pos_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
2917 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x + ( 2 * TreePanel.MOVE ) + getXdistance()
2921 pos_x = node.getXcoord() + x + 2 + half_box_size;
2924 if ( !using_visual_font ) {
2925 pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) );
2928 pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
2930 if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM
2931 && ( node.isExternal() || node.isCollapse() ) ) {
2932 drawConnection( node.getXcoord(), pos_x - x, node.getYcoord(), 5, 20, g, to_pdf );
2933 if ( node.isCollapse() ) {
2937 final String sb_str = _sb.toString();
2938 // GUILHEM_BEG ______________
2939 if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
2940 && ( _query_sequence != null ) ) {
2941 x = paintSequenceRelation( g, node, x, half_box_size, pos_x, pos_y, sb_str );
2943 // GUILHEM_END _____________
2944 if ( sb_str.length() > 0 ) {
2945 if ( !isAllowAttributedStrings() ) {
2946 TreePanel.drawString( sb_str, pos_x, pos_y, g );
2949 drawStringX( sb_str, pos_x, pos_y, g );
2952 if ( _sb.length() > 0 ) {
2953 if ( !using_visual_font && !is_in_found_nodes ) {
2954 x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
2957 x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
2960 if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
2961 && ( node.getNodeData().getSequence().getAnnotations() != null )
2962 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
2963 final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
2964 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2965 g.setColor( Color.BLACK );
2967 else if ( getControlPanel().isColorAccordingToAnnotation() ) {
2968 g.setColor( calculateColorForAnnotation( ann ) );
2970 final String ann_str = TreePanelUtil.createAnnotationString( ann,
2971 getOptions().isShowAnnotationRefSource() );
2972 TreePanel.drawString( ann_str,
2973 node.getXcoord() + x + 3 + half_box_size,
2975 + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ),
2978 _sb.append( ann_str );
2979 if ( _sb.length() > 0 ) {
2980 if ( !using_visual_font && !is_in_found_nodes ) {
2981 x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
2984 x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
2988 if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
2989 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
2990 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
2991 if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
2992 && node.getNodeData().isHasBinaryCharacters() ) {
2993 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
2994 g.setColor( Color.BLACK );
2997 g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() );
2999 if ( getControlPanel().isShowBinaryCharacters() ) {
3000 TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
3002 node.getXcoord() + x + 1 + half_box_size,
3003 node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
3004 / down_shift_factor ),
3006 paintGainedAndLostCharacters( g,
3008 node.getNodeData().getBinaryCharacters()
3009 .getGainedCharactersAsStringBuffer().toString(),
3010 node.getNodeData().getBinaryCharacters()
3011 .getLostCharactersAsStringBuffer().toString() );
3014 TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
3015 node.getXcoord() + x + 4 + half_box_size,
3016 node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
3017 / down_shift_factor ),
3019 paintGainedAndLostCharacters( g,
3021 "+" + node.getNodeData().getBinaryCharacters().getGainedCount(),
3022 "-" + node.getNodeData().getBinaryCharacters().getLostCount() );
3029 private final int paintSequenceRelation( final Graphics2D g,
3030 final PhylogenyNode node,
3032 final int half_box_size,
3035 final String sb_str ) {
3036 int nodeTextBoundsWidth = 0;
3037 if ( sb_str.length() > 0 ) {
3038 final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how...
3039 nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth();
3041 if ( node.getNodeData().getSequence().equals( _query_sequence ) ) {
3042 if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence
3043 g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 );
3044 g.setColor( getTreeColorSet().getBackgroundColor() );
3048 final List<SequenceRelation> seqRelations = node.getNodeData().getSequence().getSequenceRelations();
3049 for( final SequenceRelation seqRelation : seqRelations ) {
3050 final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence )
3051 || seqRelation.getRef1().isEqual( _query_sequence ) )
3052 && seqRelation.getType()
3053 .equals( getControlPanel().getSequenceRelationTypeBox().getSelectedItem() );
3054 if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
3055 final double linePosX = node.getXcoord() + 2 + half_box_size;
3056 final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence()
3057 || ( seqRelation.getConfidence() == null ) ) ? null
3058 : " (" + seqRelation.getConfidence().getValue() + ")";
3059 if ( sConfidence != null ) {
3060 float confidenceX = pos_x;
3061 if ( sb_str.length() > 0 ) {
3062 confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
3063 + CONFIDENCE_LEFT_MARGIN;
3065 if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
3066 final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
3067 .getBounds().getWidth();
3068 TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
3069 x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
3072 if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */
3074 if ( nodeTextBoundsWidth == 0 ) {
3075 nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */
3078 nodeTextBoundsWidth += 2;
3080 g.drawLine( ( int ) linePosX + 1,
3082 ( int ) linePosX + x + nodeTextBoundsWidth,
3083 3 + ( int ) pos_y );
3092 private final void drawConnection( final float x1,
3095 final int dist_left,
3096 final int dist_right,
3098 final boolean pdf ) {
3099 if ( ( ( x1 + dist_left ) < ( x2 - dist_right ) ) ) {
3100 final Stroke strok = g.getStroke();
3102 if ( strok == STROKE_005 ) {
3103 g.setStroke( STROKE_001_DASHED );
3105 else if ( strok == STROKE_01 ) {
3106 g.setStroke( STROKE_005_DASHED );
3109 g.setStroke( STROKE_01_DASHED );
3113 g.setColor( lighter( col ) );
3115 drawLine( x1 + dist_left, y, x2 - dist_right, y, g );
3116 g.setStroke( strok );
3123 public static Color lighter( final Color color ) {
3124 if ( ( color.getRed() == 0 ) && ( color.getGreen() == 0 ) && ( color.getBlue() == 0 ) ) {
3125 return new Color( 200, 200, 200 );
3132 private final void addLabelForCollapsed( final String first,
3135 final PhylogenyNode node ) {
3136 _sb.append( first.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? first
3137 : first.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) );
3138 _sb.append( " ... " );
3139 _sb.append( last.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? last
3140 : last.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) );
3141 _sb.append( " (" + size + ")" );
3142 if ( _found_nodes_0 != null || _found_nodes_1 != null ) {
3145 int[] res = calcFoundNodesInSubtree( node );
3146 if ( res[ 0 ] > 0 ) {
3148 _sb.append( res[ 0 ] );
3150 _sb.append( res[ 1 ] );
3156 private final int[] calcFoundNodesInSubtree( final PhylogenyNode node ) {
3157 final List<PhylogenyNode> all_descs = PhylogenyMethods.getAllDescendants( node );
3158 int res[] = new int[ 2 ];
3161 for( final PhylogenyNode desc : all_descs ) {
3162 if ( desc.isHasNodeData() ) {
3163 if ( ( _found_nodes_0 != null && _found_nodes_0.contains( desc.getId() ) )
3164 || ( _found_nodes_1 != null && _found_nodes_1.contains( desc.getId() ) ) ) {
3175 private final boolean isAllowAttributedStrings() {
3179 final private void paintNodeDataUnrootedCirc( final Graphics2D g,
3180 final PhylogenyNode node,
3181 final boolean to_pdf,
3182 final boolean to_graphics_file,
3183 final boolean radial_labels,
3184 final double ur_angle,
3185 final boolean is_in_found_nodes ) {
3186 if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
3191 if ( node.getNodeData().isHasTaxonomy()
3192 && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames()
3193 || getControlPanel().isShowTaxonomyCommonNames() ) ) {
3194 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3195 if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
3196 _sb.append( taxonomy.getTaxonomyCode() );
3199 if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
3200 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
3201 && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3202 _sb.append( taxonomy.getScientificName() );
3204 _sb.append( taxonomy.getCommonName() );
3207 else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3208 _sb.append( taxonomy.getScientificName() );
3211 else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3212 _sb.append( taxonomy.getCommonName() );
3216 else if ( _control_panel.isShowTaxonomyScientificNames() ) {
3217 if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
3218 _sb.append( taxonomy.getScientificName() );
3222 else if ( _control_panel.isShowTaxonomyCommonNames() ) {
3223 if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
3224 _sb.append( taxonomy.getCommonName() );
3229 if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
3231 _sb.append( node.getAllExternalDescendants().size() );
3234 if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
3235 if ( _sb.length() > 0 ) {
3238 _sb.append( node.getName() );
3240 if ( node.getNodeData().isHasSequence() ) {
3241 if ( getControlPanel().isShowSequenceAcc()
3242 && ( node.getNodeData().getSequence().getAccession() != null ) ) {
3243 if ( _sb.length() > 0 ) {
3246 if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
3247 _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
3250 _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
3252 if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
3253 if ( _sb.length() > 0 ) {
3256 _sb.append( node.getNodeData().getSequence().getName() );
3259 //g.setFont( getTreeFontSet().getLargeFont() );
3260 //if ( is_in_found_nodes ) {
3261 // g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
3263 if ( _sb.length() > 1 ) {
3264 setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
3265 final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
3266 final String sb_str = _sb.toString();
3268 if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
3269 m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI;
3272 m = ( float ) ( ur_angle % TWO_PI );
3274 _at = g.getTransform();
3275 boolean need_to_reset = false;
3276 final float x_coord = node.getXcoord();
3278 if ( !using_visual_font ) {
3279 y_coord = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / 3.0f );
3282 y_coord = node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / 3.0f );
3284 if ( radial_labels ) {
3285 need_to_reset = true;
3286 boolean left = false;
3287 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3291 g.rotate( m, x_coord, node.getYcoord() );
3293 if ( !using_visual_font ) {
3294 g.translate( -( getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth() ),
3298 g.translate( -( getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth() ), 0 );
3303 if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
3304 need_to_reset = true;
3305 if ( !using_visual_font ) {
3306 g.translate( -getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth(), 0 );
3309 g.translate( -getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth(), 0 );
3313 TreePanel.drawString( sb_str, x_coord, y_coord, g );
3314 if ( need_to_reset ) {
3315 g.setTransform( _at );
3320 final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
3321 if ( node.isCollapse() ) {
3324 if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
3325 g.setColor( getColorForFoundNode( node ) );
3326 drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
3327 node.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
3328 OVERVIEW_FOUND_NODE_BOX_SIZE,
3329 OVERVIEW_FOUND_NODE_BOX_SIZE,
3333 if ( !node.isExternal() && !node.isCollapse() ) {
3334 boolean first_child = true;
3336 //final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node );
3337 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3338 final PhylogenyNode child_node = node.getChildNode( i );
3339 final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3340 if ( first_child ) {
3341 first_child = false;
3342 y2 = node.getYSecondary() - ( getOvYDistance()
3343 * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
3346 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3348 final float x2 = calculateOvBranchLengthToParent( child_node, factor_x );
3349 new_x = x2 + node.getXSecondary();
3350 final float diff_y = node.getYSecondary() - y2;
3351 final float diff_x = node.getXSecondary() - new_x;
3352 if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) {
3353 paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node );
3355 child_node.setXSecondary( new_x );
3356 child_node.setYSecondary( y2 );
3357 y2 += getOvYDistance() * child_node.getNumberOfExternalNodes();
3362 final private void paintNodeRectangular( final Graphics2D g,
3363 final PhylogenyNode node,
3364 final boolean to_pdf,
3365 final boolean dynamically_hide,
3366 final int dynamic_hiding_factor,
3367 final boolean to_graphics_file,
3368 final boolean disallow_shortcutting ) {
3369 final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
3370 if ( node.isCollapse() ) {
3371 if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
3372 paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
3376 if ( node.isExternal() ) {
3377 ++_external_node_index;
3379 // Confidence values
3380 if ( getControlPanel().isShowConfidenceValues() && !node.isExternal() && !node.isRoot()
3381 && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
3382 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
3383 || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
3384 && node.getBranchData().isHasConfidences() ) {
3385 paintConfidenceValues( g, node, to_pdf, to_graphics_file );
3387 // Draw a line to root:
3388 if ( node.isRoot() && _phylogeny.isRooted() ) {
3389 paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file );
3392 float new_x_min = Float.MAX_VALUE;
3393 float min_dist = 1.5f;
3394 if ( !disallow_shortcutting ) {
3395 if ( dynamic_hiding_factor > 4000 ) {
3398 else if ( dynamic_hiding_factor > 1000 ) {
3401 else if ( dynamic_hiding_factor > 100 ) {
3405 if ( !node.isExternal() && !node.isCollapse() ) {
3406 boolean first_child = true;
3408 for( int i = 0; i < node.getNumberOfDescendants(); ++i ) {
3409 final PhylogenyNode child_node = node.getChildNode( i );
3410 final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes();
3411 if ( first_child ) {
3412 first_child = false;
3413 y2 = node.getYcoord() - ( _y_distance
3414 * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) );
3417 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3419 final float x2 = calculateBranchLengthToParent( child_node, factor_x );
3420 new_x = x2 + node.getXcoord();
3421 if ( dynamically_hide && ( x2 < new_x_min ) ) {
3424 final float diff_y = node.getYcoord() - y2;
3425 final float diff_x = node.getXcoord() - new_x;
3426 if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist )
3427 || ( diff_x < -min_dist ) ) {
3428 paintBranchRectangular( g,
3437 child_node.setXcoord( new_x );
3438 child_node.setYcoord( y2 );
3439 y2 += _y_distance * child_node.getNumberOfExternalNodes();
3441 paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
3443 if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
3444 && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
3445 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
3446 paintMolecularSequences( g, node, to_pdf );
3448 if ( dynamically_hide && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) )
3449 || ( !node.isExternal() && ( ( new_x_min < 20 )
3450 || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont()
3451 .getHeight() ) ) ) ) ) {
3454 final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes, 0 );
3455 paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf );
3458 final private void paintNodeWithRenderableData( final int x,
3460 final PhylogenyNode node,
3461 final boolean to_graphics_file,
3462 final boolean to_pdf ) {
3463 if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) {
3466 if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) {
3469 if ( ( !getControlPanel().isShowExternalData() && node.isExternal() ) ) {
3472 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
3473 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) && ( node.getNodeData()
3474 .getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
3475 RenderableDomainArchitecture rds = null;
3477 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
3479 catch ( final ClassCastException cce ) {
3480 cce.printStackTrace();
3482 if ( rds != null ) {
3483 final int default_height = 7;
3484 float y = getYdistance();
3485 if ( getControlPanel().isDynamicallyHideData() ) {
3486 y = getTreeFontSet().getFontMetricsLarge().getHeight();
3488 final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height;
3489 rds.setRenderingHeight( h > 1 ? h : 2 );
3490 if ( getControlPanel().isDrawPhylogram() ) {
3491 if ( getOptions().isLineUpRendarableNodeData() ) {
3492 if ( getOptions().isRightLineUpDomains() ) {
3493 rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
3494 + _length_of_longest_text + 50 //TODO why plus 50?
3495 + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ) ),
3496 node.getYcoord() - ( h / 2.0f ),
3502 rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
3503 + _length_of_longest_text + 50 ),
3504 node.getYcoord() - ( h / 2.0f ),
3511 rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
3515 if ( getOptions().isRightLineUpDomains() ) {
3516 rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text )
3517 - 20 ) + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ),
3518 node.getYcoord() - ( h / 2.0f ),
3524 rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
3525 node.getYcoord() - ( h / 2.0f ),
3533 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
3534 && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) {
3535 final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(),
3536 getStatisticsForExpressionValues(),
3537 getConfiguration() );
3539 double domain_add = 0;
3540 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
3541 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
3542 domain_add = _domain_structure_width + 10;
3544 if ( getControlPanel().isDrawPhylogram() ) {
3545 rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
3548 rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text
3549 + domain_add ), node.getYcoord() - 3, g, this, to_pdf );
3553 //if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
3554 // && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
3555 // && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
3556 // paintMolecularSequences( g, node, to_pdf );
3560 final private void paintOvRectangle( final Graphics2D g ) {
3561 final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
3562 final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
3563 final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
3564 final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
3565 final float width = getOvMaxWidth() / w_ratio;
3566 final float height = getOvMaxHeight() / h_ratio;
3567 final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
3568 final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
3569 g.setColor( getTreeColorSet().getFoundColor0() );
3570 getOvRectangle().setRect( x, y, width, height );
3571 final Stroke s = g.getStroke();
3572 g.setStroke( STROKE_1 );
3573 if ( ( width < 6 ) && ( height < 6 ) ) {
3574 drawRectFilled( x, y, 6, 6, g );
3575 getOvVirtualRectangle().setRect( x, y, 6, 6 );
3577 else if ( width < 6 ) {
3578 drawRectFilled( x, y, 6, height, g );
3579 getOvVirtualRectangle().setRect( x, y, 6, height );
3581 else if ( height < 6 ) {
3582 drawRectFilled( x, y, width, 6, g );
3583 getOvVirtualRectangle().setRect( x, y, width, 6 );
3586 drawRect( x, y, width, height, g );
3587 if ( isInOvRect() ) {
3588 drawRect( x + 1, y + 1, width - 2, height - 2, g );
3590 getOvVirtualRectangle().setRect( x, y, width, height );
3595 final private void paintPhylogenyLite( final Graphics2D g ) {
3596 _phylogeny.getRoot().setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition()
3597 + ( MOVE / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ) );
3598 _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
3599 final Stroke s = g.getStroke();
3600 g.setStroke( STROKE_05 );
3601 for( final PhylogenyNode element : _nodes_in_preorder ) {
3602 paintNodeLite( g, element );
3605 paintOvRectangle( g );
3609 * Paint the root branch. (Differs from others because it will always be a
3610 * single horizontal line).
3611 * @param to_graphics_file
3613 * @return new x1 value
3615 final private void paintRootBranch( final Graphics2D g,
3618 final PhylogenyNode root,
3619 final boolean to_pdf,
3620 final boolean to_graphics_file ) {
3621 assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file );
3622 float d = getXdistance();
3623 if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) {
3624 d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() );
3626 if ( d < MIN_ROOT_LENGTH ) {
3627 d = MIN_ROOT_LENGTH;
3629 if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) {
3630 drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g );
3633 final double w = PhylogenyMethods.getBranchWidthValue( root );
3634 drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
3636 paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
3639 final private void paintScale( final Graphics2D g,
3642 final boolean to_pdf,
3643 final boolean to_graphics_file ) {
3645 final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() );
3647 final int y2 = y1 - 8;
3648 final int y3 = y1 - 4;
3649 g.setFont( getTreeFontSet().getSmallFont() );
3650 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3651 g.setColor( Color.BLACK );
3654 g.setColor( getTreeColorSet().getBranchLengthColor() );
3656 final Stroke s = g.getStroke();
3657 g.setStroke( STROKE_1 );
3658 drawLine( x1, y1, x1, y2, g );
3659 drawLine( x2, y1, x2, y2, g );
3660 drawLine( x1, y3, x2, y3, g );
3661 if ( getScaleLabel() != null ) {
3662 g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
3667 final private int paintTaxonomy( final Graphics2D g,
3668 final PhylogenyNode node,
3669 final boolean is_in_found_nodes,
3670 final boolean to_pdf,
3671 final boolean to_graphics_file,
3672 final float x_shift ) {
3673 final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
3674 final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
3675 setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() );
3676 float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
3677 if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM
3678 && node.isExternal() ) {
3679 start_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
3680 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift + ( 2 * TreePanel.MOVE ) + getXdistance()
3684 if ( !using_visual_font ) {
3685 start_y = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent()
3686 / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
3689 start_y = node.getYcoord()
3690 + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
3693 nodeTaxonomyDataAsSB( taxonomy, _sb );
3694 final String label = _sb.toString();
3696 if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
3697 && ( node.getNodeData().isHasSequence() )
3698 && node.getNodeData().getSequence().equals( _query_sequence ) ) {
3699 // invert font color and background color to show that this is the query sequence
3700 final Rectangle2D nodeTextBounds = new TextLayout( label,
3702 new FontRenderContext( null, false, false ) )
3704 g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
3705 g.setColor( getTreeColorSet().getBackgroundColor() );
3708 TreePanel.drawString( label, start_x, start_y, g );
3709 if ( !using_visual_font && !is_in_found_nodes ) {
3710 return getFontMetricsForLargeDefaultFont().stringWidth( label );
3712 return getFontMetrics( g.getFont() ).stringWidth( label );
3715 final private void paintUnrooted( final PhylogenyNode n,
3716 final double low_angle,
3717 final double high_angle,
3718 final boolean radial_labels,
3720 final boolean to_pdf,
3721 final boolean to_graphics_file ) {
3723 n.setXcoord( getWidth() / 2 );
3724 n.setYcoord( getHeight() / 2 );
3726 if ( n.isExternal() ) {
3727 paintNodeDataUnrootedCirc( g,
3732 ( high_angle + low_angle ) / 2,
3733 isInFoundNodes( n ) || isInCurrentExternalNodes( n ) );
3736 final float num_enclosed = n.getNumberOfExternalNodes();
3737 final float x = n.getXcoord();
3738 final float y = n.getYcoord();
3739 double current_angle = low_angle;
3740 // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20;
3741 // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20;
3742 // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20;
3743 // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20;
3744 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
3745 final PhylogenyNode desc = n.getChildNode( i );
3746 /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) )
3747 // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) )
3748 // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) )
3749 // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) {
3752 //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) {
3755 //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) {
3758 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
3759 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
3761 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
3762 if ( desc.getDistanceToParent() < 0 ) {
3766 length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() );
3770 length = getUrtFactor();
3772 final double mid_angle = current_angle + ( arc_size / 2 );
3773 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
3774 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
3775 desc.setXcoord( new_x );
3776 desc.setYcoord( new_y );
3777 paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
3778 current_angle += arc_size;
3779 assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
3780 drawLine( x, y, new_x, new_y, g );
3781 paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file );
3784 paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
3788 final private void paintUnrootedLite( final PhylogenyNode n,
3789 final double low_angle,
3790 final double high_angle,
3792 final float urt_ov_factor ) {
3794 final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) );
3795 final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) );
3796 n.setXSecondary( x_pos );
3797 n.setYSecondary( y_pos );
3799 if ( n.isExternal() ) {
3802 final float num_enclosed = n.getNumberOfExternalNodes();
3803 final float x = n.getXSecondary();
3804 final float y = n.getYSecondary();
3805 double current_angle = low_angle;
3806 for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
3807 final PhylogenyNode desc = n.getChildNode( i );
3808 final int desc_num_enclosed = desc.getNumberOfExternalNodes();
3809 final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle );
3811 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
3812 if ( desc.getDistanceToParent() < 0 ) {
3816 length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor );
3820 length = urt_ov_factor;
3822 final double mid_angle = current_angle + ( arc_size / 2 );
3823 final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) );
3824 final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) );
3825 desc.setXSecondary( new_x );
3826 desc.setYSecondary( new_y );
3827 if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
3828 g.setColor( getColorForFoundNode( desc ) );
3829 drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
3830 desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
3831 OVERVIEW_FOUND_NODE_BOX_SIZE,
3832 OVERVIEW_FOUND_NODE_BOX_SIZE,
3834 g.setColor( getTreeColorSet().getOvColor() );
3836 paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor );
3837 current_angle += arc_size;
3838 drawLine( x, y, new_x, new_y, g );
3842 final private void pasteSubtree( final PhylogenyNode node ) {
3843 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
3844 errorMessageNoCutCopyPasteInUnrootedDisplay();
3847 if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) {
3848 JOptionPane.showMessageDialog( this,
3849 "No tree in buffer (need to copy or cut a subtree first)",
3850 "Attempt to paste with empty buffer",
3851 JOptionPane.ERROR_MESSAGE );
3854 final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() );
3855 final Object[] options = { "As sibling", "As descendant", "Cancel" };
3856 final int r = JOptionPane.showOptionDialog( this,
3857 "How to paste subtree" + label + "?",
3859 JOptionPane.CLOSED_OPTION,
3860 JOptionPane.QUESTION_MESSAGE,
3864 boolean paste_as_sibling = true;
3866 paste_as_sibling = false;
3868 else if ( r != 0 ) {
3871 final Phylogeny buffer_phy = getCutOrCopiedTree().copy();
3872 buffer_phy.setAllNodesToNotCollapse();
3873 PhylogenyMethods.preOrderReId( buffer_phy );
3874 buffer_phy.setRooted( true );
3875 boolean need_to_show_whole = false;
3876 if ( paste_as_sibling ) {
3877 if ( node.isRoot() ) {
3878 JOptionPane.showMessageDialog( this,
3879 "Cannot paste sibling to root",
3880 "Attempt to paste sibling to root",
3881 JOptionPane.ERROR_MESSAGE );
3884 buffer_phy.addAsSibling( node );
3887 if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) {
3888 need_to_show_whole = true;
3889 _phylogeny = buffer_phy;
3892 buffer_phy.addAsChild( node );
3895 if ( getCopiedAndPastedNodes() == null ) {
3896 setCopiedAndPastedNodes( new HashSet<Long>() );
3898 final List<PhylogenyNode> nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy );
3899 final Set<Long> node_ids = new HashSet<Long>( nodes.size() );
3900 for( final PhylogenyNode n : nodes ) {
3901 node_ids.add( n.getId() );
3903 node_ids.add( node.getId() );
3904 getCopiedAndPastedNodes().addAll( node_ids );
3905 setNodeInPreorderToNull();
3906 _phylogeny.externalNodesHaveChanged();
3907 _phylogeny.clearHashIdToNodeMap();
3908 _phylogeny.recalculateNumberOfExternalDescendants( true );
3909 resetNodeIdToDistToLeafMap();
3911 if ( need_to_show_whole ) {
3912 getControlPanel().showWhole();
3917 private final StringBuffer propertiesToString( final PhylogenyNode node ) {
3918 return node.getNodeData().getProperties().asText();
3921 private void setColor( final Graphics2D g,
3922 final PhylogenyNode node,
3923 final boolean to_graphics_file,
3924 final boolean to_pdf,
3925 final boolean is_in_found_nodes,
3926 final Color default_color ) {
3927 if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
3928 g.setColor( Color.BLACK );
3930 else if ( is_in_found_nodes ) {
3931 g.setColor( getColorForFoundNode( node ) );
3933 else if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
3934 && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
3935 g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
3937 else if ( getControlPanel().isColorAccordingToSequence() ) {
3938 g.setColor( getSequenceBasedColor( node ) );
3940 else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
3941 g.setColor( getTaxonomyBasedColor( node ) );
3943 else if ( getControlPanel().isColorAccordingToAnnotation()
3944 && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null )
3945 && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
3946 g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
3948 else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
3949 && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
3950 g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
3952 else if ( to_pdf ) {
3953 g.setColor( Color.BLACK );
3956 g.setColor( default_color );
3960 final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
3961 getMainPanel().setCopiedAndPastedNodes( nodeIds );
3964 final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) {
3965 getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
3968 private boolean setFont( final Graphics2D g, final PhylogenyNode node, final boolean is_in_found_nodes ) {
3969 Font visual_font = null;
3970 if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) {
3971 visual_font = node.getNodeData().getNodeVisualData().getFont();
3972 g.setFont( visual_font != null ? visual_font : getTreeFontSet().getLargeFont() );
3975 g.setFont( getTreeFontSet().getLargeFont() );
3977 if ( is_in_found_nodes ) {
3978 g.setFont( g.getFont().deriveFont( Font.BOLD ) );
3980 return visual_font != null;
3983 final private void setInOv( final boolean in_ov ) {
3987 final private void setOvMaxHeight( final float ov_max_height ) {
3988 _ov_max_height = ov_max_height;
3991 final private void setOvMaxWidth( final float ov_max_width ) {
3992 _ov_max_width = ov_max_width;
3995 final private void setOvXcorrectionFactor( final float f ) {
3996 _ov_x_correction_factor = f;
3999 final private void setOvXDistance( final float ov_x_distance ) {
4000 _ov_x_distance = ov_x_distance;
4003 final private void setOvXPosition( final int ov_x_position ) {
4004 _ov_x_position = ov_x_position;
4007 final private void setOvYDistance( final float ov_y_distance ) {
4008 _ov_y_distance = ov_y_distance;
4011 final private void setOvYPosition( final int ov_y_position ) {
4012 _ov_y_position = ov_y_position;
4015 final private void setOvYStart( final int ov_y_start ) {
4016 _ov_y_start = ov_y_start;
4019 final private void setScaleDistance( final double scale_distance ) {
4020 _scale_distance = scale_distance;
4023 final private void setScaleLabel( final String scale_label ) {
4024 _scale_label = scale_label;
4027 private final void setupStroke( final Graphics2D g ) {
4028 if ( getYdistance() < 0.0001 ) {
4029 g.setStroke( STROKE_0025 );
4031 if ( getYdistance() < 0.001 ) {
4032 g.setStroke( STROKE_005 );
4034 else if ( getYdistance() < 0.01 ) {
4035 g.setStroke( STROKE_01 );
4037 else if ( getYdistance() < 0.5 ) {
4038 g.setStroke( STROKE_025 );
4040 else if ( getYdistance() < 1 ) {
4041 g.setStroke( STROKE_05 );
4043 else if ( getYdistance() < 2 ) {
4044 g.setStroke( STROKE_075 );
4046 else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) {
4047 g.setStroke( STROKE_1 );
4050 g.setStroke( STROKE_2 );
4054 final private void setUpUrtFactor() {
4055 final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
4056 : getVisibleRect().height;
4057 if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) {
4058 setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) );
4061 final int max_depth = _circ_max_depth;
4062 if ( max_depth > 0 ) {
4063 setUrtFactor( d / ( 2 * max_depth ) );
4066 setUrtFactor( d / 2 );
4069 setUrtFactorOv( getUrtFactor() );
4072 final private void setUrtFactor( final float urt_factor ) {
4073 _urt_factor = urt_factor;
4076 final private void setUrtFactorOv( final float urt_factor_ov ) {
4077 _urt_factor_ov = urt_factor_ov;
4080 private void showExtDescNodeData( final PhylogenyNode node, final char separator ) {
4081 final List<String> data = new ArrayList<String>();
4082 final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
4083 if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
4084 for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
4085 if ( !nodes.contains( n ) ) {
4090 for( final PhylogenyNode n : nodes ) {
4091 switch ( getOptions().getExtDescNodeDataToReturn() ) {
4093 if ( !ForesterUtil.isEmpty( n.getName() ) ) {
4094 data.add( n.getName() );
4098 if ( n.getNodeData().isHasSequence()
4099 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
4100 data.add( n.getNodeData().getSequence().getName() );
4104 if ( n.getNodeData().isHasSequence()
4105 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
4106 data.add( n.getNodeData().getSequence().getGeneName() );
4109 case SEQUENCE_SYMBOL:
4110 if ( n.getNodeData().isHasSequence()
4111 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
4112 data.add( n.getNodeData().getSequence().getSymbol() );
4115 case SEQUENCE_MOL_SEQ_FASTA:
4116 final StringBuilder sb = new StringBuilder();
4117 if ( n.getNodeData().isHasSequence()
4118 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
4119 final StringBuilder ann = new StringBuilder();
4120 if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( n.getName() ) ) {
4121 ann.append( n.getName() );
4122 ann.append( separator );
4124 if ( n.getNodeData().isHasTaxonomy() ) {
4125 if ( getControlPanel().isShowTaxonomyCode()
4126 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
4127 ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
4128 ann.append( separator );
4130 if ( getControlPanel().isShowTaxonomyScientificNames()
4131 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
4132 ann.append( n.getNodeData().getTaxonomy().getScientificName() );
4133 ann.append( separator );
4135 if ( getControlPanel().isShowTaxonomyCommonNames()
4136 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
4137 ann.append( n.getNodeData().getTaxonomy().getCommonName() );
4138 ann.append( separator );
4141 if ( getControlPanel().isShowSeqSymbols()
4142 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
4143 ann.append( n.getNodeData().getSequence().getSymbol() );
4144 ann.append( separator );
4146 if ( getControlPanel().isShowSeqNames()
4147 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
4148 ann.append( n.getNodeData().getSequence().getName() );
4149 ann.append( separator );
4151 if ( getControlPanel().isShowGeneNames()
4152 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
4153 ann.append( n.getNodeData().getSequence().getGeneName() );
4154 ann.append( separator );
4156 if ( getControlPanel().isShowSequenceAcc()
4157 && n.getNodeData().getSequence().getAccession() != null ) {
4158 ann.append( n.getNodeData().getSequence().getAccession().asText() );
4159 ann.append( separator );
4162 final String ann_str;
4163 if ( ann.length() > 0 && ann.charAt( ann.length() - 1 ) == separator ) {
4164 ann_str = ann.substring( 0, ann.length() - 1 );
4167 ann_str = ann.toString();
4169 sb.append( SequenceWriter.toFasta( ann_str,
4170 n.getNodeData().getSequence().getMolecularSequence(),
4172 data.add( sb.toString() );
4176 if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null )
4177 && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) {
4178 data.add( n.getNodeData().getSequence().getAccession().toString() );
4181 case TAXONOMY_SCIENTIFIC_NAME:
4182 if ( n.getNodeData().isHasTaxonomy()
4183 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
4184 data.add( n.getNodeData().getTaxonomy().getScientificName() );
4188 if ( n.getNodeData().isHasTaxonomy()
4189 && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
4190 data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() );
4194 case DOMAINS_COLLAPSED_PER_PROTEIN:
4195 if ( n.getNodeData().isHasSequence()
4196 && ( n.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4197 final DomainArchitecture da = n.getNodeData().getSequence().getDomainArchitecture();
4198 final Set<String> s = new HashSet<String>();
4199 for( int i = 0; i < da.getDomains().size(); ++i ) {
4200 final ProteinDomain d = da.getDomain( i );
4201 if ( d.getConfidence() <= Math.pow( 10, getDomainStructureEvalueThresholdExp() ) ) {
4202 final String name = d.getName();
4203 if ( !( s.contains( name ) ) ) {
4206 .getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) {
4214 case SEQ_ANNOTATIONS:
4215 if ( n.getNodeData().isHasSequence() ) {
4216 if ( n.getNodeData().isHasSequence()
4217 && ( n.getNodeData().getSequence().getAnnotations() != null ) ) {
4218 final SortedSet<Annotation> a = n.getNodeData().getSequence().getAnnotations();
4219 for( int i = 0; i < a.size(); ++i ) {
4220 data.add( n.getNodeData().getSequence().getAnnotation( i ).toString() );
4226 if ( n.getNodeData().isHasSequence() ) {
4227 if ( n.getNodeData().isHasSequence()
4228 && ( n.getNodeData().getSequence().getAnnotations() != null ) ) {
4229 final SortedSet<Annotation> a = n.getNodeData().getSequence().getAnnotations();
4230 for( int i = 0; i < a.size(); ++i ) {
4231 final Annotation ann = n.getNodeData().getSequence().getAnnotation( i );
4232 final String ref = ann.getRef();
4233 if ( ref.toUpperCase().startsWith( "GO:" ) ) {
4241 TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
4244 throw new IllegalArgumentException( "unknown data element: "
4245 + getOptions().getExtDescNodeDataToReturn() );
4248 final StringBuilder sb = new StringBuilder();
4249 final int size = TreePanelUtil.nodeDataIntoStringBuffer( data, getOptions(), sb );
4250 if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
4251 || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
4252 if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
4253 System.out.println( sb );
4255 if ( sb.length() < 1 ) {
4256 clearCurrentExternalNodesDataBuffer();
4259 setCurrentExternalNodesDataBuffer( sb );
4262 else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
4263 if ( sb.length() < 1 ) {
4264 TreePanelUtil.showInformationMessage( this,
4265 "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
4266 "Descendants of selected node do not contain selected data" );
4267 clearCurrentExternalNodesDataBuffer();
4270 setCurrentExternalNodesDataBuffer( sb );
4272 if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
4273 title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
4274 : obtainTitleForExtDescNodeData() ) + " for " + data.size() + " nodes, unique entries: "
4278 title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data"
4279 : obtainTitleForExtDescNodeData() ) + " for " + data.size() + "/"
4280 + node.getNumberOfExternalNodes() + " external descendats of node " + node
4281 + ", unique entries: " + size;
4283 final String s = sb.toString().trim();
4284 getMainPanel().getMainFrame().showTextFrame( s, title );
4289 final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
4291 if ( ( node.getName().length() > 0 )
4292 || ( node.getNodeData().isHasTaxonomy()
4293 && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
4294 || ( node.getNodeData().isHasSequence()
4295 && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) )
4296 || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
4297 || node.getBranchData().isHasConfidences() ) {
4298 _popup_buffer.setLength( 0 );
4300 if ( node.getName().length() > 0 ) {
4302 _popup_buffer.append( node.getName() );
4304 if ( node.getNodeData().isHasTaxonomy()
4305 && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
4307 boolean enc_data = false;
4308 final Taxonomy tax = node.getNodeData().getTaxonomy();
4309 if ( _popup_buffer.length() > 0 ) {
4310 _popup_buffer.append( "\n" );
4312 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
4313 _popup_buffer.append( "[" );
4314 _popup_buffer.append( tax.getTaxonomyCode() );
4315 _popup_buffer.append( "]" );
4318 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
4320 _popup_buffer.append( " " );
4322 _popup_buffer.append( tax.getScientificName() );
4325 if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
4327 _popup_buffer.append( " (" );
4330 _popup_buffer.append( "(" );
4332 _popup_buffer.append( tax.getCommonName() );
4333 _popup_buffer.append( ")" );
4336 if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) {
4338 _popup_buffer.append( " (" );
4341 _popup_buffer.append( "(" );
4343 _popup_buffer.append( tax.getAuthority() );
4344 _popup_buffer.append( ")" );
4347 if ( !ForesterUtil.isEmpty( tax.getRank() ) ) {
4349 _popup_buffer.append( " [" );
4352 _popup_buffer.append( "[" );
4354 _popup_buffer.append( tax.getRank() );
4355 _popup_buffer.append( "]" );
4358 if ( tax.getSynonyms().size() > 0 ) {
4360 _popup_buffer.append( " " );
4362 _popup_buffer.append( "[" );
4364 for( final String syn : tax.getSynonyms() ) {
4365 if ( !ForesterUtil.isEmpty( syn ) ) {
4367 _popup_buffer.append( syn );
4368 if ( counter < tax.getSynonyms().size() ) {
4369 _popup_buffer.append( ", " );
4374 _popup_buffer.append( "]" );
4377 if ( ( tax.getIdentifier() != null )
4378 && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
4379 if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) {
4380 _popup_buffer.append( "[" );
4381 _popup_buffer.append( tax.getIdentifier().getProvider() );
4382 _popup_buffer.append( "] " );
4384 _popup_buffer.append( tax.getIdentifier().getValue() );
4388 if ( node.getNodeData().isHasSequence()
4389 && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
4391 boolean enc_data = false;
4392 if ( _popup_buffer.length() > 0 ) {
4393 _popup_buffer.append( "\n" );
4395 final Sequence seq = node.getNodeData().getSequence();
4396 if ( seq.getAccession() != null ) {
4397 _popup_buffer.append( "[" );
4398 if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) {
4399 _popup_buffer.append( seq.getAccession().getSource() );
4400 _popup_buffer.append( ":" );
4402 _popup_buffer.append( seq.getAccession().getValue() );
4403 _popup_buffer.append( "]" );
4406 if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) {
4408 _popup_buffer.append( " [" );
4411 _popup_buffer.append( "[" );
4413 _popup_buffer.append( seq.getSymbol() );
4414 _popup_buffer.append( "]" );
4417 if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
4419 _popup_buffer.append( " [" );
4422 _popup_buffer.append( "[" );
4424 _popup_buffer.append( seq.getGeneName() );
4425 _popup_buffer.append( "]" );
4428 if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
4430 _popup_buffer.append( " " );
4432 _popup_buffer.append( seq.getName() );
4435 if ( node.getNodeData().isHasDate() ) {
4437 if ( _popup_buffer.length() > 0 ) {
4438 _popup_buffer.append( "\n" );
4440 _popup_buffer.append( node.getNodeData().getDate().asSimpleText() );
4442 if ( node.getNodeData().isHasDistribution() ) {
4444 if ( _popup_buffer.length() > 0 ) {
4445 _popup_buffer.append( "\n" );
4447 _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() );
4449 if ( node.getBranchData().isHasConfidences() ) {
4450 final List<Confidence> confs = node.getBranchData().getConfidences();
4451 for( final Confidence confidence : confs ) {
4453 if ( _popup_buffer.length() > 0 ) {
4454 _popup_buffer.append( "\n" );
4456 if ( !ForesterUtil.isEmpty( confidence.getType() ) ) {
4457 _popup_buffer.append( "[" );
4458 _popup_buffer.append( confidence.getType() );
4459 _popup_buffer.append( "] " );
4461 _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
4463 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
4464 if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
4465 _popup_buffer.append( " (sd=" );
4466 _popup_buffer.append( FORMATTER_CONFIDENCE
4467 .format( ForesterUtil.round( confidence.getStandardDeviation(),
4469 .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
4470 _popup_buffer.append( ")" );
4474 if ( node.getNodeData().isHasProperties() ) {
4475 if ( _popup_buffer.length() > 0 ) {
4476 _popup_buffer.append( "\n" );
4478 _popup_buffer.append( node.getNodeData().getProperties().asText() );
4480 if ( _popup_buffer.length() > 0 ) {
4481 if ( !getConfiguration().isUseNativeUI() ) {
4483 .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
4484 _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
4485 if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
4486 _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
4488 else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
4489 _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
4491 else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
4492 _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
4495 _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
4499 _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) );
4501 _rollover_popup.setText( _popup_buffer.toString() );
4502 _node_desc_popup = PopupFactory.getSharedInstance()
4505 e.getLocationOnScreen().x + 10,
4506 e.getLocationOnScreen().y - ( lines * 20 ) );
4507 _node_desc_popup.show();
4511 catch ( final Exception ex ) {
4516 final private void showNodeEditFrame( final PhylogenyNode n ) {
4517 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4518 // pop up edit box for single node
4519 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" );
4520 _node_frame_index++;
4523 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4527 final private void showNodeFrame( final PhylogenyNode n ) {
4528 if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) {
4529 // pop up edit box for single node
4530 _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index );
4531 _node_frame_index++;
4534 JOptionPane.showMessageDialog( this, "too many node windows are open" );
4538 final private void switchDisplaygetPhylogenyGraphicsType() {
4539 switch ( getPhylogenyGraphicsType() ) {
4541 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
4542 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE );
4545 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
4546 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED );
4549 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
4550 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED );
4553 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
4554 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR );
4557 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
4558 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX );
4561 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
4562 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
4565 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
4566 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR );
4569 setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
4570 getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
4573 throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() );
4575 if ( getControlPanel().getDynamicallyHideData() != null ) {
4576 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4577 getControlPanel().getDynamicallyHideData().setEnabled( false );
4580 getControlPanel().getDynamicallyHideData().setEnabled( true );
4583 if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
4584 getControlPanel().setDrawPhylogramEnabled( true );
4587 getControlPanel().setDrawPhylogramEnabled( false );
4589 getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
4592 final void calcMaxDepth() {
4593 if ( _phylogeny != null ) {
4594 _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
4599 * Set parameters for printing the displayed tree
4602 final void calcParametersForPainting( final int x, final int y ) {
4603 // updateStyle(); not needed?
4604 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
4606 calculateLongestExtNodeInfo();
4607 if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) )
4608 && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
4609 while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) )
4610 && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) {
4611 getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), true );
4612 calculateLongestExtNodeInfo();
4616 while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) ) && ( getTreeFontSet().getLargeFont()
4617 .getSize() <= ( getTreeFontSet().getLargeFontMemory().getSize()
4618 - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) {
4619 getMainPanel().getTreeFontSet().increaseFontSize();
4620 calculateLongestExtNodeInfo();
4623 //_length_of_longest_text = calcLengthOfLongestText();
4624 int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
4625 final int max_depth = PhylogenyMethods.calculateMaxDepthConsiderCollapsed( _phylogeny ) + 1;
4626 if ( ext_nodes == 1 ) {
4627 ext_nodes = max_depth;
4628 if ( ext_nodes < 1 ) {
4635 if ( !isNonLinedUpCladogram() ) {
4636 xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) );
4637 ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) );
4640 xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) );
4641 ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) );
4643 float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) );
4644 if ( xdist < 0.0 ) {
4647 if ( ov_xdist < 0.0 ) {
4650 if ( ydist < 0.0 ) {
4653 setXdistance( xdist );
4654 setYdistance( ydist );
4655 setOvXDistance( ov_xdist );
4656 final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() );
4657 //final double height = PhylogenyMethods.calculateMaxDepth( _phylogeny );
4659 final float corr = ( float ) ( ( x - ( 2.0 * TreePanel.MOVE ) - getLongestExtNodeInfo()
4660 - getXdistance() ) / height );
4661 setXcorrectionFactor( corr > 0 ? corr : 0 );
4662 final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height );
4663 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
4666 setXcorrectionFactor( 0 );
4667 setOvXcorrectionFactor( 0 );
4669 _circ_max_depth = max_depth;
4672 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
4673 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
4674 // int dynamic_hiding_factor = calcDynamicHidingFactor();
4675 // if ( dynamic_hiding_factor > 1 ) {
4676 // while ( dynamic_hiding_factor > 1
4677 // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) {
4678 // getTreeFontSet().decreaseFontSize( 1, true );
4679 // dynamic_hiding_factor = calcDynamicHidingFactor();
4682 // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) {
4683 // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) {
4684 // getTreeFontSet().increaseFontSize();
4685 // dynamic_hiding_factor = calcDynamicHidingFactor();
4693 final void calculateLongestExtNodeInfo() {
4694 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
4697 int max_possible_length = ForesterUtil
4698 .roundToInt( ( getSize().getWidth() - ( 2 * MOVE ) ) * AptxConstants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
4699 if ( max_possible_length < 20 ) {
4700 max_possible_length = 20;
4703 int longest_txt = 0;
4704 _longest_domain = 0;
4705 PhylogenyNode longest_txt_node = _phylogeny.getFirstExternalNode();
4706 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
4708 if ( node.isCollapse() ) {
4711 final StringBuilder sb = new StringBuilder();
4712 nodeDataAsSB( node, sb );
4713 if ( node.getNodeData().isHasTaxonomy() ) {
4714 nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb );
4716 final int txt = sb.length();
4717 if ( txt > longest_txt ) {
4719 longest_txt_node = node;
4721 boolean use_vis = false;
4722 final Graphics2D g = ( Graphics2D ) getGraphics();
4723 if ( getControlPanel().isUseVisualStyles() ) {
4724 use_vis = setFont( g, node, false );
4727 sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
4730 sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() );
4732 if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
4733 sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
4734 .getGainedCharactersAsStringBuffer().toString() );
4736 if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
4737 && ( node.getNodeData().getVector().size() > 0 ) ) {
4738 if ( getConfiguration() != null ) {
4739 sum += getConfiguration().getVectorDataWidth() + 10;
4742 sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10;
4745 if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence()
4746 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
4748 // TODO this might need some clean up
4749 final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture();
4750 sum += ( ( _domain_structure_width
4751 / ( ( RenderableDomainArchitecture ) d ).getOriginalSize().getWidth() ) * d.getTotalLength() )
4753 if ( d.getTotalLength() > _longest_domain ) {
4754 _longest_domain = d.getTotalLength();
4757 if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() )
4758 && ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
4759 && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
4761 sum += RenderableMsaSequence.DEFAULT_WIDTH + 30;
4763 if ( sum >= max_possible_length ) {
4764 _longest_ext_node_info = max_possible_length;
4765 // return; //FIXME why?
4767 if ( sum > longest ) {
4771 _ext_node_with_longest_txt_info = longest_txt_node;
4772 if ( longest >= max_possible_length ) {
4773 _longest_ext_node_info = max_possible_length;
4776 _longest_ext_node_info = longest;
4778 _length_of_longest_text = calcLengthOfLongestText();
4781 final void calculateScaleDistance() {
4782 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
4785 final double height = getMaxDistanceToRoot();
4787 if ( ( height <= 0.5 ) ) {
4788 setScaleDistance( 0.01 );
4790 else if ( height <= 5.0 ) {
4791 setScaleDistance( 0.1 );
4793 else if ( height <= 50.0 ) {
4794 setScaleDistance( 1 );
4796 else if ( height <= 500.0 ) {
4797 setScaleDistance( 10 );
4800 setScaleDistance( 100 );
4804 setScaleDistance( 0.0 );
4806 String scale_label = String.valueOf( getScaleDistance() );
4807 if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) {
4808 scale_label += " [" + _phylogeny.getDistanceUnit() + "]";
4810 setScaleLabel( scale_label );
4813 final Color calculateSequenceBasedColor( final Sequence seq ) {
4814 if ( ForesterUtil.isEmpty( seq.getName() ) ) {
4815 return getTreeColorSet().getSequenceColor();
4818 final String seq_name = seq.getName();
4819 c = getControlPanel().getSequenceColors().get( seq_name );
4821 c = AptxUtil.calculateColorFromString( seq_name, false );
4822 getControlPanel().getSequenceColors().put( seq_name, c );
4827 final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
4828 if ( getOptions().isColorByTaxonomicGroup() ) {
4829 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
4831 String group = null;
4833 group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
4835 catch ( final Exception e ) {
4838 if ( !ex && !ForesterUtil.isEmpty( group ) ) {
4839 final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
4845 return getTreeColorSet().getTaxonomyColor();
4848 if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
4849 return getTreeColorSet().getTaxonomyColor();
4852 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
4853 c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
4855 if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
4856 c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
4859 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
4860 c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
4861 getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
4864 c = AptxUtil.calculateColorFromString( tax.getScientificName(), true );
4865 getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
4872 void clearCurrentExternalNodesDataBuffer() {
4873 setCurrentExternalNodesDataBuffer( new StringBuilder() );
4877 * Collapse the tree from the given node
4882 final void collapse( final PhylogenyNode node ) {
4883 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4884 JOptionPane.showMessageDialog( this,
4885 "Cannot collapse in unrooted display type",
4886 "Attempt to collapse in unrooted display",
4887 JOptionPane.WARNING_MESSAGE );
4890 if ( !node.isExternal() && !node.isRoot() ) {
4891 final boolean collapse = !node.isCollapse();
4892 TreePanelUtil.collapseSubtree( node, collapse );
4893 updateSetOfCollapsedExternalNodes();
4894 _phylogeny.recalculateNumberOfExternalDescendants( true );
4895 resetNodeIdToDistToLeafMap();
4896 calculateLongestExtNodeInfo();
4897 setNodeInPreorderToNull();
4898 _control_panel.displayedPhylogenyMightHaveChanged( true );
4899 resetPreferredSize();
4901 _main_panel.adjustJScrollPane();
4906 final void uncollapseAll( final PhylogenyNode node ) {
4907 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
4908 JOptionPane.showMessageDialog( this,
4909 "Cannot uncollapse in unrooted display type",
4910 "Attempt to uncollapse in unrooted display",
4911 JOptionPane.WARNING_MESSAGE );
4914 if ( !node.isExternal() ) {
4915 TreePanelUtil.uncollapseSubtree( node );
4916 updateSetOfCollapsedExternalNodes();
4917 _phylogeny.recalculateNumberOfExternalDescendants( true );
4918 resetNodeIdToDistToLeafMap();
4919 calculateLongestExtNodeInfo();
4920 setNodeInPreorderToNull();
4921 _control_panel.displayedPhylogenyMightHaveChanged( true );
4922 resetPreferredSize();
4924 _main_panel.adjustJScrollPane();
4929 final void collapseSpeciesSpecificSubtrees() {
4930 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
4934 TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
4935 updateSetOfCollapsedExternalNodes();
4936 _phylogeny.recalculateNumberOfExternalDescendants( true );
4937 resetNodeIdToDistToLeafMap();
4938 calculateLongestExtNodeInfo();
4939 setNodeInPreorderToNull();
4940 resetPreferredSize();
4941 resetDepthCollapseDepthValue();
4942 resetRankCollapseRankValue();
4943 _main_panel.adjustJScrollPane();
4944 getControlPanel().showWhole();
4948 final void colorRank( final String rank ) {
4949 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
4953 AptxUtil.removeBranchColors( _phylogeny );
4954 final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
4955 if ( colorizations > 0 ) {
4956 _control_panel.setColorBranches( true );
4957 if ( _control_panel.getUseVisualStylesCb() != null ) {
4958 _control_panel.getUseVisualStylesCb().setSelected( true );
4960 if ( _control_panel.getColorAccSpeciesCb() != null ) {
4961 _control_panel.getColorAccSpeciesCb().setSelected( false );
4963 _options.setColorLabelsSameAsParentBranch( true );
4964 if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) {
4965 getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true );
4967 _control_panel.repaint();
4971 if ( colorizations > 0 ) {
4972 String msg = "Taxonomy colorization via " + rank + " completed:\n";
4973 if ( colorizations > 1 ) {
4974 msg += "colorized " + colorizations + " subtrees";
4977 msg += "colorized one subtree";
4980 JOptionPane.showMessageDialog( this,
4982 "Taxonomy Rank-Colorization Completed (" + rank + ")",
4983 JOptionPane.INFORMATION_MESSAGE );
4986 String msg = "Could not taxonomy rank-colorize any subtree via " + rank + ".\n";
4987 msg += "Possible solutions (given that suitable taxonomic information is present):\n";
4988 msg += "select a different rank (e.g. phylum, genus, ...)\n";
4990 msg += "execute:\n";
4991 msg += "1. \"" + MainFrame.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
4992 msg += "2. \"" + MainFrame.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
4993 JOptionPane.showMessageDialog( this,
4995 "Taxonomy Rank-Colorization Failed",
4996 JOptionPane.WARNING_MESSAGE );
5000 final void confColor() {
5001 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
5005 AptxUtil.removeBranchColors( _phylogeny );
5006 TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
5007 _control_panel.setColorBranches( true );
5008 if ( _control_panel.getUseVisualStylesCb() != null ) {
5009 _control_panel.getUseVisualStylesCb().setSelected( true );
5015 final void decreaseDomainStructureEvalueThresholdExp() {
5016 if ( _domain_structure_e_value_thr_exp > -20 ) {
5017 _domain_structure_e_value_thr_exp -= 1;
5022 * Find the node, if any, at the given location
5026 * @return pointer to the node at x,y, null if not found
5028 final PhylogenyNode findNode( final int x, final int y ) {
5029 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
5032 final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE;
5033 for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
5034 final PhylogenyNode node = iter.next();
5035 if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
5036 && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
5037 && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
5038 && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
5039 && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
5046 final Configuration getConfiguration() {
5047 return _configuration;
5050 final ControlPanel getControlPanel() {
5051 return _control_panel;
5054 String getCurrentExternalNodesDataBufferAsString() {
5055 return _current_external_nodes_data_buffer.toString();
5058 int getCurrentExternalNodesDataBufferChangeCounter() {
5059 return _current_external_nodes_data_buffer_change_counter;
5062 final int getDomainStructureEvalueThresholdExp() {
5063 return _domain_structure_e_value_thr_exp;
5066 final Set<Long> getFoundNodes0() {
5067 return _found_nodes_0;
5070 final Set<Long> getFoundNodes1() {
5071 return _found_nodes_1;
5074 List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
5075 final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
5076 if ( getFoundNodes0() != null ) {
5077 for( final Long id : getFoundNodes0() ) {
5078 final PhylogenyNode n = _phylogeny.getNode( id );
5080 additional_nodes.add( n );
5084 if ( getFoundNodes1() != null ) {
5085 for( final Long id : getFoundNodes1() ) {
5086 if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
5087 final PhylogenyNode n = _phylogeny.getNode( id );
5089 additional_nodes.add( n );
5094 return additional_nodes;
5097 final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
5098 if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
5099 return ( PhylogenyMethods.getBranchColorValue( node ) );
5102 return ( getTreeColorSet().getBranchColor() );
5106 final int getLongestExtNodeInfo() {
5107 return _longest_ext_node_info;
5110 final Options getOptions() {
5111 if ( _options == null ) {
5112 _options = getControlPanel().getOptions();
5117 final Rectangle2D getOvRectangle() {
5118 return _ov_rectangle;
5121 final Rectangle getOvVirtualRectangle() {
5122 return _ov_virtual_rectangle;
5125 final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
5126 return _graphics_type;
5129 final Color getSequenceBasedColor( final PhylogenyNode node ) {
5130 if ( node.getNodeData().isHasSequence() ) {
5131 return calculateSequenceBasedColor( node.getNodeData().getSequence() );
5133 // return non-colorized color
5134 return getTreeColorSet().getSequenceColor();
5137 final double getStartingAngle() {
5138 return _urt_starting_angle;
5141 DescriptiveStatistics getStatisticsForExpressionValues() {
5142 return _statistics_for_vector_data;
5145 final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
5146 if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) {
5147 return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
5149 // return non-colorized color
5150 return getTreeColorSet().getTaxonomyColor();
5153 final File getTreeFile() {
5157 final float getXcorrectionFactor() {
5158 return _x_correction_factor;
5161 final float getXdistance() {
5165 final float getYdistance() {
5169 final void increaseDomainStructureEvalueThresholdExp() {
5170 if ( _domain_structure_e_value_thr_exp < 3 ) {
5171 _domain_structure_e_value_thr_exp += 1;
5175 final void initNodeData() {
5176 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
5179 double _max_original_domain_structure_width = 0.0;
5180 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
5181 if ( node.getNodeData().isHasSequence()
5182 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
5183 RenderableDomainArchitecture rds = null;
5184 if ( !( node.getNodeData().getSequence()
5185 .getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
5186 if ( SPECIAL_DOMAIN_COLORING ) {
5187 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
5188 .getDomainArchitecture(), node.getName() );
5191 rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
5192 .getDomainArchitecture() );
5194 node.getNodeData().getSequence().setDomainArchitecture( rds );
5197 rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture();
5199 if ( getControlPanel().isShowDomainArchitectures() ) {
5200 final double dsw = rds.getOriginalSize().getWidth();
5201 if ( dsw > _max_original_domain_structure_width ) {
5202 _max_original_domain_structure_width = dsw;
5207 if ( getControlPanel().isShowDomainArchitectures() ) {
5208 final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width );
5209 for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) {
5210 if ( node.getNodeData().isHasSequence()
5211 && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
5212 final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData()
5213 .getSequence().getDomainArchitecture();
5214 rds.setRenderingFactorWidth( ds_factor_width );
5215 rds.setParameter( _domain_structure_e_value_thr_exp );
5221 final boolean inOv( final MouseEvent e ) {
5222 return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
5223 && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
5224 && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) )
5225 && ( e.getY() < ( ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
5228 final boolean inOvRectangle( final MouseEvent e ) {
5229 return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
5230 && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
5231 && ( e.getY() >= ( getOvRectangle().getY() - 1 ) )
5232 && ( e.getY() <= ( getOvRectangle().getY() + getOvRectangle().getHeight() + 1 ) ) );
5235 final boolean isCanCollapse() {
5236 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5239 final boolean isCanUncollapseAll( final PhylogenyNode node ) {
5240 if ( node.isExternal() || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) {
5243 if ( node.isCollapse() ) {
5246 final PhylogenyNodeIterator it = new PreorderTreeIterator( node );
5247 while ( it.hasNext() ) {
5248 if ( it.next().isCollapse() ) {
5255 final boolean isCanColorSubtree() {
5256 return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
5259 final boolean isCanCopy() {
5260 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
5263 final boolean isCanCut( final PhylogenyNode node ) {
5264 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
5265 && !node.isRoot() );
5268 final boolean isCanDelete() {
5269 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() );
5272 final boolean isCanPaste() {
5273 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable()
5274 && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() );
5277 final boolean isCanReroot() {
5278 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) );
5281 final boolean isCanSubtree( final PhylogenyNode node ) {
5282 return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal()
5283 && ( !node.isRoot() || ( _subtree_index > 0 ) ) );
5286 final boolean isCurrentTreeIsSubtree() {
5287 return ( _subtree_index > 0 );
5290 final boolean isEdited() {
5294 final boolean isInOvRect() {
5298 final boolean isOvOn() {
5302 final boolean isPhyHasBranchLengths() {
5303 return _phy_has_branch_lengths;
5306 final void midpointRoot() {
5307 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
5310 if ( !_phylogeny.isRerootable() ) {
5311 JOptionPane.showMessageDialog( this,
5312 "This is not rerootable",
5314 JOptionPane.WARNING_MESSAGE );
5317 setNodeInPreorderToNull();
5319 PhylogenyMethods.midpointRoot( _phylogeny );
5320 resetNodeIdToDistToLeafMap();
5326 final void mouseClicked( final MouseEvent e ) {
5327 if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) {
5328 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
5329 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
5330 double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) )
5332 double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) )
5340 final double max_x = getWidth() - getVisibleRect().width;
5341 final double max_y = getHeight() - getVisibleRect().height;
5348 getMainPanel().getCurrentScrollPane().getViewport()
5349 .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
5350 setInOvRect( true );
5354 final PhylogenyNode node = findNode( e.getX(), e.getY() );
5355 if ( node != null ) {
5356 if ( !node.isRoot() && node.getParent().isCollapse() ) {
5359 _highlight_node = node;
5360 // Check if shift key is down
5361 if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
5362 // Yes, so add to _found_nodes
5363 if ( getFoundNodes0() == null ) {
5364 setFoundNodes0( new HashSet<Long>() );
5366 getFoundNodes0().add( node.getId() );
5367 // Check if control key is down
5369 else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
5370 // Yes, so pop-up menu
5371 displayNodePopupMenu( node, e.getX(), e.getY() );
5372 // Handle unadorned click
5375 // Check for right mouse button
5376 if ( e.getModifiers() == 4 ) {
5377 displayNodePopupMenu( node, e.getX(), e.getY() );
5380 // if not in _found_nodes, clear _found_nodes
5381 handleClickToAction( _control_panel.getActionWhenNodeClicked(), node );
5386 // no node was clicked
5387 _highlight_node = null;
5393 final void mouseDragInBrowserPanel( final MouseEvent e ) {
5394 setCursor( MOVE_CURSOR );
5395 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
5396 scroll_position.x -= ( e.getX() - getLastDragPointX() );
5397 scroll_position.y -= ( e.getY() - getLastDragPointY() );
5398 if ( scroll_position.x < 0 ) {
5399 scroll_position.x = 0;
5402 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
5403 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
5404 if ( scroll_position.x > max_x ) {
5405 scroll_position.x = max_x;
5408 if ( scroll_position.y < 0 ) {
5409 scroll_position.y = 0;
5412 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
5413 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
5414 if ( scroll_position.y > max_y ) {
5415 scroll_position.y = max_y;
5418 if ( isOvOn() || getOptions().isShowScale() ) {
5421 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
5424 final void mouseDragInOvRectangle( final MouseEvent e ) {
5425 setCursor( HAND_CURSOR );
5426 final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth();
5427 final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight();
5428 final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition();
5429 double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) );
5430 double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) );
5431 scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx );
5432 scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy );
5433 if ( scroll_position.x <= 0 ) {
5434 scroll_position.x = 0;
5438 final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum()
5439 - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount();
5440 if ( scroll_position.x >= max_x ) {
5442 scroll_position.x = max_x;
5445 if ( scroll_position.y <= 0 ) {
5447 scroll_position.y = 0;
5450 final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum()
5451 - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount();
5452 if ( scroll_position.y >= max_y ) {
5454 scroll_position.y = max_y;
5458 getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position );
5459 setLastMouseDragPointX( ( float ) ( e.getX() + dx ) );
5460 setLastMouseDragPointY( ( float ) ( e.getY() + dy ) );
5463 final void mouseMoved( final MouseEvent e ) {
5464 requestFocusInWindow();
5465 if ( _current_external_nodes != null ) {
5466 _current_external_nodes = null;
5469 if ( getControlPanel().isNodeDescPopup() ) {
5470 if ( _node_desc_popup != null ) {
5471 _node_desc_popup.hide();
5472 _node_desc_popup = null;
5475 if ( getOptions().isShowOverview() && isOvOn() ) {
5476 if ( inOvVirtualRectangle( e ) ) {
5477 if ( !isInOvRect() ) {
5478 setInOvRect( true );
5483 if ( isInOvRect() ) {
5484 setInOvRect( false );
5489 if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) {
5498 final PhylogenyNode node = findNode( e.getX(), e.getY() );
5499 if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) {
5500 if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) {
5501 for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
5502 addToCurrentExternalNodes( n.getId() );
5504 setCursor( HAND_CURSOR );
5507 else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE )
5508 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE )
5509 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE )
5510 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE )
5511 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT )
5512 || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) {
5513 setCursor( CUT_CURSOR );
5516 setCursor( HAND_CURSOR );
5517 if ( getControlPanel().isNodeDescPopup() ) {
5518 showNodeDataPopup( e, node );
5523 setCursor( ARROW_CURSOR );
5528 final void mouseReleasedInBrowserPanel( final MouseEvent e ) {
5529 setCursor( ARROW_CURSOR );
5532 final void multiplyUrtFactor( final float f ) {
5536 final void paintBranchCircular( final PhylogenyNode p,
5537 final PhylogenyNode c,
5539 final boolean radial_labels,
5540 final boolean to_pdf,
5541 final boolean to_graphics_file ) {
5542 final double angle = _urt_nodeid_angle_map.get( c.getId() );
5543 final double root_x = _root.getXcoord();
5544 final double root_y = _root.getYcoord();
5545 final double dx = root_x - p.getXcoord();
5546 final double dy = root_y - p.getYcoord();
5547 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
5548 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
5549 assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file );
5550 if ( ( c.isFirstChildNode() || c.isLastChildNode() )
5551 && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) {
5552 final double r2 = 2.0 * parent_radius;
5553 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
5555 drawLine( c.getXcoord(),
5557 root_x + ( Math.cos( angle ) * parent_radius ),
5558 root_y + ( Math.sin( angle ) * parent_radius ),
5560 paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
5561 if ( c.isExternal() ) {
5562 final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c )
5563 || isInCurrentExternalNodes( c );
5564 if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
5565 && ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
5568 paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes );
5572 final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) {
5573 final double angle = _urt_nodeid_angle_map.get( c.getId() );
5574 final double root_x = _root.getXSecondary();
5575 final double root_y = _root.getYSecondary();
5576 final double dx = root_x - p.getXSecondary();
5577 final double dy = root_y - p.getYSecondary();
5578 final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle;
5579 final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) );
5580 g.setColor( getTreeColorSet().getOvColor() );
5581 if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) {
5582 final double r2 = 2.0 * parent_radius;
5583 drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g );
5585 drawLine( c.getXSecondary(),
5587 root_x + ( Math.cos( angle ) * parent_radius ),
5588 root_y + ( Math.sin( angle ) * parent_radius ),
5590 if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
5591 g.setColor( getColorForFoundNode( c ) );
5592 drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
5593 c.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF,
5594 OVERVIEW_FOUND_NODE_BOX_SIZE,
5595 OVERVIEW_FOUND_NODE_BOX_SIZE,
5600 final void paintCircular( final Phylogeny phy,
5601 final double starting_angle,
5606 final boolean to_pdf,
5607 final boolean to_graphics_file ) {
5608 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
5609 System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
5610 _root = phy.getRoot();
5611 _root.setXcoord( center_x );
5612 _root.setYcoord( center_y );
5613 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
5614 double current_angle = starting_angle;
5616 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
5617 final PhylogenyNode n = it.next();
5618 if ( !n.isCollapse() ) {
5619 n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
5620 n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
5621 _urt_nodeid_angle_map.put( n.getId(), current_angle );
5622 _urt_nodeid_index_map.put( n.getId(), i++ );
5623 current_angle += ( TWO_PI / circ_num_ext_nodes );
5627 System.out.println( "is collapse" + n.getName() );
5630 paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
5631 paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file );
5634 final void paintCircularLite( final Phylogeny phy,
5635 final double starting_angle,
5639 final Graphics2D g ) {
5640 final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
5641 _root = phy.getRoot();
5642 _root.setXSecondary( center_x );
5643 _root.setYSecondary( center_y );
5644 double current_angle = starting_angle;
5645 for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
5646 final PhylogenyNode n = it.next();
5647 n.setXSecondary( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
5648 n.setYSecondary( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
5649 _urt_nodeid_angle_map.put( n.getId(), current_angle );
5650 current_angle += ( TWO_PI / circ_num_ext_nodes );
5652 paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
5655 final void paintPhylogeny( final Graphics2D g,
5656 final boolean to_pdf,
5657 final boolean to_graphics_file,
5658 final int graphics_file_width,
5659 final int graphics_file_height,
5660 final int graphics_file_x,
5661 final int graphics_file_y ) {
5662 if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
5665 if ( _control_panel.isShowSequenceRelations() ) {
5666 _query_sequence = _control_panel.getSelectedQuerySequence();
5668 // Color the background
5670 final Rectangle r = getVisibleRect();
5671 if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) {
5672 g.setColor( getTreeColorSet().getBackgroundColor() );
5673 if ( !to_graphics_file ) {
5677 if ( getOptions().isPrintBlackAndWhite() ) {
5678 g.setColor( Color.WHITE );
5680 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
5684 if ( !to_graphics_file ) {
5685 g.setPaint( new GradientPaint( r.x,
5687 getTreeColorSet().getBackgroundColor(),
5690 getTreeColorSet().getBackgroundColorGradientBottom() ) );
5694 g.setPaint( new GradientPaint( graphics_file_x,
5696 getTreeColorSet().getBackgroundColor(),
5698 graphics_file_y + graphics_file_height,
5699 getTreeColorSet().getBackgroundColorGradientBottom() ) );
5700 g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
5706 g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
5708 if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED )
5709 && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) {
5710 _external_node_index = 0;
5711 // Position starting X of tree
5712 if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/ ) {
5713 _phylogeny.getRoot().setXcoord( TreePanel.MOVE );
5715 else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) {
5716 _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE
5717 + ( _phylogeny.getRoot().getDistanceToParent() * getXcorrectionFactor() ) ) );
5720 _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() );
5722 // Position starting Y of tree
5723 _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
5724 + ( TreePanel.MOVE / 2.0f ) );
5725 final int dynamic_hiding_factor = calcDynamicHidingFactor();
5726 if ( getControlPanel().isDynamicallyHideData() ) {
5727 if ( dynamic_hiding_factor > 1 ) {
5728 getControlPanel().setDynamicHidingIsOn( true );
5731 getControlPanel().setDynamicHidingIsOn( false );
5734 if ( _nodes_in_preorder == null ) {
5735 _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ];
5737 for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) {
5738 _nodes_in_preorder[ i++ ] = it.next();
5741 final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 )
5742 /* || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()*/ //TODO check if this is really not needed.
5743 || to_graphics_file || to_pdf;
5744 for( final PhylogenyNode element : _nodes_in_preorder ) {
5745 paintNodeRectangular( g,
5748 getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ),
5749 dynamic_hiding_factor,
5751 disallow_shortcutting );
5753 if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) {
5754 if ( !( to_graphics_file || to_pdf ) ) {
5757 getVisibleRect().y + getVisibleRect().height,
5762 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
5765 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
5766 paintPhylogenyLite( g );
5769 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5770 if ( getControlPanel().getDynamicallyHideData() != null ) {
5771 getControlPanel().setDynamicHidingIsOn( false );
5773 final double angle = getStartingAngle();
5774 final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
5775 _dynamic_hiding_factor = 0;
5776 if ( getControlPanel().isDynamicallyHideData() ) {
5777 _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5
5778 * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
5780 if ( getControlPanel().getDynamicallyHideData() != null ) {
5781 if ( _dynamic_hiding_factor > 1 ) {
5782 getControlPanel().setDynamicHidingIsOn( true );
5785 getControlPanel().setDynamicHidingIsOn( false );
5788 paintUnrooted( _phylogeny.getRoot(),
5790 ( float ) ( angle + ( 2 * Math.PI ) ),
5795 if ( getOptions().isShowScale() ) {
5796 if ( !( to_graphics_file || to_pdf ) ) {
5799 getVisibleRect().y + getVisibleRect().height,
5804 paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file );
5807 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
5808 g.setColor( getTreeColorSet().getOvColor() );
5809 paintUnrootedLite( _phylogeny.getRoot(),
5811 angle + ( 2 * Math.PI ),
5813 ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) );
5814 paintOvRectangle( g );
5817 else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
5818 final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() )
5819 / 2 ) - ( MOVE + getLongestExtNodeInfo() ) );
5820 final int d = radius + MOVE + getLongestExtNodeInfo();
5821 _dynamic_hiding_factor = 0;
5822 if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
5823 _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5
5824 * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
5826 if ( getControlPanel().getDynamicallyHideData() != null ) {
5827 if ( _dynamic_hiding_factor > 1 ) {
5828 getControlPanel().setDynamicHidingIsOn( true );
5831 getControlPanel().setDynamicHidingIsOn( false );
5834 paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file );
5835 if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) {
5836 final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2
5837 : getOvMaxWidth() / 2 );
5838 double x_scale = 1.0;
5839 double y_scale = 1.0;
5840 int x_pos = getVisibleRect().x + getOvXPosition();
5841 int y_pos = getVisibleRect().y + getOvYPosition();
5842 if ( getWidth() > getHeight() ) {
5843 x_scale = ( double ) getHeight() / getWidth();
5844 x_pos = ForesterUtil.roundToInt( x_pos / x_scale );
5847 y_scale = ( double ) getWidth() / getHeight();
5848 y_pos = ForesterUtil.roundToInt( y_pos / y_scale );
5850 _at = g.getTransform();
5851 g.scale( x_scale, y_scale );
5852 paintCircularLite( _phylogeny,
5856 ( int ) ( radius_ov - ( getLongestExtNodeInfo()
5857 / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ),
5859 g.setTransform( _at );
5860 paintOvRectangle( g );
5865 final void recalculateMaxDistanceToRoot() {
5866 _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() );
5867 if ( getPhylogeny().getRoot().getDistanceToParent() > 0 ) {
5868 _max_distance_to_root += getPhylogeny().getRoot().getDistanceToParent();
5873 * Remove all edit-node frames
5875 final void removeAllEditNodeJFrames() {
5876 for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) {
5877 if ( _node_frames[ i ] != null ) {
5878 _node_frames[ i ].dispose();
5879 _node_frames[ i ] = null;
5882 _node_frame_index = 0;
5886 * Remove a node-edit frame.
5888 final void removeEditNodeFrame( final int i ) {
5889 _node_frame_index--;
5890 _node_frames[ i ] = null;
5891 if ( i < _node_frame_index ) {
5892 for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) {
5893 _node_frames[ j ] = _node_frames[ j + 1 ];
5895 _node_frames[ _node_frame_index ] = null;
5899 final void reRoot( final PhylogenyNode node ) {
5900 if ( !getPhylogeny().isRerootable() ) {
5901 JOptionPane.showMessageDialog( this,
5902 "This is not rerootable",
5904 JOptionPane.WARNING_MESSAGE );
5907 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
5908 JOptionPane.showMessageDialog( this,
5909 "Cannot reroot in unrooted display type",
5910 "Attempt to reroot tree in unrooted display",
5911 JOptionPane.WARNING_MESSAGE );
5914 getPhylogeny().reRoot( node );
5915 getPhylogeny().recalculateNumberOfExternalDescendants( true );
5916 resetNodeIdToDistToLeafMap();
5917 setNodeInPreorderToNull();
5918 resetPreferredSize();
5919 getMainPanel().adjustJScrollPane();
5922 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
5923 getControlPanel().showWhole();
5927 final void resetNodeIdToDistToLeafMap() {
5928 _nodeid_dist_to_leaf = new HashMap<Long, Short>();
5931 final void resetPreferredSize() {
5932 if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) {
5938 + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 );
5939 if ( getControlPanel().isDrawPhylogram() ) {
5940 x = TreePanel.MOVE + getLongestExtNodeInfo()
5941 + ForesterUtil.roundToInt( ( getXcorrectionFactor()
5942 * getPhylogeny().calculateHeight( !_options.isCollapsedWithAverageHeigh() ) )
5946 if ( !isNonLinedUpCladogram() ) {
5947 x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil
5948 .roundToInt( getXdistance() * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
5951 x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil
5952 .roundToInt( getXdistance() * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
5955 setPreferredSize( new Dimension( x, y ) );
5958 final void selectNode( final PhylogenyNode node ) {
5959 if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
5960 getFoundNodes0().remove( node.getId() );
5961 getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
5962 if ( getFoundNodes0().size() < 1 ) {
5963 getControlPanel().searchReset0();
5967 getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
5968 getControlPanel().getSearchResetButton0().setEnabled( true );
5969 getControlPanel().getSearchResetButton0().setVisible( true );
5970 if ( getFoundNodes0() == null ) {
5971 setFoundNodes0( new HashSet<Long>() );
5973 getFoundNodes0().add( node.getId() );
5974 getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
5978 final void setArrowCursor() {
5979 setCursor( ARROW_CURSOR );
5983 final void setControlPanel( final ControlPanel atv_control ) {
5984 _control_panel = atv_control;
5987 void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) {
5988 increaseCurrentExternalNodesDataBufferChangeCounter();
5989 _current_external_nodes_data_buffer = sb;
5992 final void setFoundNodes0( final Set<Long> found_nodes ) {
5993 _found_nodes_0 = found_nodes;
5996 final void setFoundNodes1( final Set<Long> found_nodes ) {
5997 _found_nodes_1 = found_nodes;
6000 final void setInOvRect( final boolean in_ov_rect ) {
6001 _in_ov_rect = in_ov_rect;
6004 final void setLargeFonts() {
6005 getTreeFontSet().largeFonts();
6008 final void setLastMouseDragPointX( final float x ) {
6009 _last_drag_point_x = x;
6012 final void setLastMouseDragPointY( final float y ) {
6013 _last_drag_point_y = y;
6016 final void setMediumFonts() {
6017 getTreeFontSet().mediumFonts();
6020 final void setNodeInPreorderToNull() {
6021 _nodes_in_preorder = null;
6024 final void setOvOn( final boolean ov_on ) {
6028 final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) {
6029 _graphics_type = graphics_type;
6033 final void setSmallFonts() {
6034 getTreeFontSet().smallFonts();
6037 final void setStartingAngle( final double starting_angle ) {
6038 _urt_starting_angle = starting_angle;
6041 void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) {
6042 _statistics_for_vector_data = statistics_for_expression_values;
6045 final void setSuperTinyFonts() {
6046 getTreeFontSet().superTinyFonts();
6049 final void setTextAntialias() {
6050 if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
6051 if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) {
6052 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY );
6055 _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED );
6058 if ( getMainPanel().getOptions().isAntialiasScreen() ) {
6059 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
6061 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
6063 // catch ( final Throwable e ) {
6064 // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
6068 _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
6069 _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
6073 final void setTinyFonts() {
6074 getTreeFontSet().tinyFonts();
6077 final void setTreeFile( final File treefile ) {
6078 _treefile = treefile;
6081 final void setXcorrectionFactor( final float f ) {
6082 _x_correction_factor = f;
6085 final void setXdistance( final float x ) {
6089 final void setYdistance( final float y ) {
6093 final void sortDescendants( final PhylogenyNode node ) {
6094 if ( !node.isExternal() ) {
6095 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
6096 if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
6097 pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
6099 else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
6100 || getControlPanel().isShowGeneNames() ) {
6101 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
6103 PhylogenyMethods.sortNodeDescendents( node, pri );
6104 setNodeInPreorderToNull();
6105 _phylogeny.externalNodesHaveChanged();
6106 _phylogeny.clearHashIdToNodeMap();
6107 _phylogeny.recalculateNumberOfExternalDescendants( true );
6108 resetNodeIdToDistToLeafMap();
6114 final void subTree( final PhylogenyNode node ) {
6115 if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
6116 JOptionPane.showMessageDialog( this,
6117 "Cannot get a sub/super tree in unrooted display",
6118 "Attempt to get sub/super tree in unrooted display",
6119 JOptionPane.WARNING_MESSAGE );
6122 if ( node.isExternal() ) {
6123 JOptionPane.showMessageDialog( this,
6124 "Cannot get a subtree of a external node",
6125 "Attempt to get subtree of external node",
6126 JOptionPane.WARNING_MESSAGE );
6129 if ( node.isRoot() && !isCurrentTreeIsSubtree() ) {
6130 JOptionPane.showMessageDialog( this,
6131 "Cannot get a subtree of the root node",
6132 "Attempt to get subtree of root node",
6133 JOptionPane.WARNING_MESSAGE );
6136 setNodeInPreorderToNull();
6137 if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) {
6138 _sub_phylogenies[ _subtree_index ] = _phylogeny;
6139 _sub_phylogenies_temp_roots[ _subtree_index ] = node;
6141 _phylogeny = TreePanelUtil.subTree( node, _phylogeny );
6142 if ( _phylogeny.getRoot().isCollapse() ) {
6143 _phylogeny.getRoot().setCollapse( false );
6145 _phylogeny.externalNodesHaveChanged();
6146 _phylogeny.clearHashIdToNodeMap();
6147 _phylogeny.recalculateNumberOfExternalDescendants( true );
6148 updateSubSuperTreeButton();
6149 getMainPanel().getControlPanel().search0();
6150 getMainPanel().getControlPanel().search1();
6151 resetRankCollapseRankValue();
6152 resetDepthCollapseDepthValue();
6153 getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
6154 getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay();
6155 getMainPanel().getControlPanel().updateRankCollapseRankDisplay();
6157 else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
6160 _main_panel.getControlPanel().showWhole();
6164 final void superTree() {
6165 setNodeInPreorderToNull();
6166 final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ];
6167 for( final PhylogenyNode n : temp_root.getDescendants() ) {
6168 n.setParent( temp_root );
6170 _sub_phylogenies[ _subtree_index ] = null;
6171 _sub_phylogenies_temp_roots[ _subtree_index ] = null;
6172 _phylogeny = _sub_phylogenies[ --_subtree_index ];
6173 _phylogeny.externalNodesHaveChanged();
6174 _phylogeny.clearHashIdToNodeMap();
6175 _phylogeny.recalculateNumberOfExternalDescendants( true );
6176 getMainPanel().getControlPanel().search0();
6177 getMainPanel().getControlPanel().search1();
6178 resetRankCollapseRankValue();
6179 resetDepthCollapseDepthValue();
6180 getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay();
6181 getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay();
6182 getMainPanel().getControlPanel().updateRankCollapseRankDisplay();
6183 updateSubSuperTreeButton();
6186 final void orderSubtree( final PhylogenyNode node ) {
6187 if ( node.isExternal() ) {
6190 DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
6191 if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
6192 pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
6194 else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols()
6195 || getControlPanel().isShowGeneNames() ) {
6196 pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
6198 PhylogenyMethods.orderAppearanceX( node, true, pri );
6199 setNodeInPreorderToNull();
6200 getPhylogeny().externalNodesHaveChanged();
6201 getPhylogeny().clearHashIdToNodeMap();
6202 getPhylogeny().recalculateNumberOfExternalDescendants( true );
6203 resetNodeIdToDistToLeafMap();
6205 getControlPanel().displayedPhylogenyMightHaveChanged( true );
6209 final void swap( final PhylogenyNode node ) {
6210 if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
6213 if ( node.getNumberOfDescendants() > 2 ) {
6214 JOptionPane.showMessageDialog( this,
6215 "Cannot swap descendants of nodes with more than 2 descendants",
6216 "Cannot swap descendants",
6217 JOptionPane.ERROR_MESSAGE );
6220 if ( !node.isExternal() ) {
6221 node.swapChildren();
6222 setNodeInPreorderToNull();
6223 _phylogeny.externalNodesHaveChanged();
6224 _phylogeny.clearHashIdToNodeMap();
6225 _phylogeny.recalculateNumberOfExternalDescendants( true );
6226 resetNodeIdToDistToLeafMap();
6232 final void taxColor() {
6233 if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
6237 TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
6238 _control_panel.setColorBranches( true );
6239 if ( _control_panel.getUseVisualStylesCb() != null ) {
6240 _control_panel.getUseVisualStylesCb().setSelected( true );
6247 final void updateOvSettings() {
6248 switch ( getOptions().getOvPlacement() ) {
6250 setOvXPosition( OV_BORDER );
6251 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
6252 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
6255 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
6256 setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) );
6257 setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) );
6260 setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) );
6261 setOvYPosition( OV_BORDER );
6262 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
6265 setOvXPosition( OV_BORDER );
6266 setOvYPosition( OV_BORDER );
6267 setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) );
6272 final void updateOvSizes() {
6273 if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) )
6274 || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) {
6276 float l = getLongestExtNodeInfo();
6277 final float w_ratio = getOvMaxWidth() / getWidth();
6279 final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes();
6280 setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) );
6282 if ( !isNonLinedUpCladogram() ) {
6283 ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) );
6286 ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) );
6288 float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) );
6289 if ( ov_xdist < 0.0 ) {
6292 if ( ydist < 0.0 ) {
6295 setOvXDistance( ov_xdist );
6296 final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() );
6298 final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height );
6299 setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 );
6302 setOvXcorrectionFactor( 0 );
6310 void updateSetOfCollapsedExternalNodes() {
6311 final Phylogeny phy = getPhylogeny();
6312 _collapsed_external_nodeid_set.clear();
6313 if ( phy != null ) {
6314 E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
6315 final PhylogenyNode ext_node = it.next();
6316 PhylogenyNode n = ext_node;
6317 while ( !n.isRoot() ) {
6318 if ( n.isCollapse() ) {
6319 _collapsed_external_nodeid_set.add( ext_node.getId() );
6320 ext_node.setCollapse( true );
6329 final void updateSubSuperTreeButton() {
6330 if ( _subtree_index < 1 ) {
6331 getControlPanel().deactivateButtonToReturnToSuperTree();
6334 getControlPanel().activateButtonToReturnToSuperTree( _subtree_index );
6338 final void updateButtonToUncollapseAll() {
6339 if ( PhylogenyMethods.isHasCollapsedNodes( _phylogeny ) ) {
6340 getControlPanel().activateButtonToUncollapseAll();
6343 getControlPanel().deactivateButtonToUncollapseAll();
6347 final void zoomInDomainStructure() {
6348 if ( _domain_structure_width < 2000 ) {
6349 _domain_structure_width *= 1.2;
6353 final void zoomOutDomainStructure() {
6354 if ( _domain_structure_width > 20 ) {
6355 _domain_structure_width *= 0.8;
6359 private final static void colorizeNodesHelper( final Color c, final PhylogenyNode node ) {
6360 if ( node.getNodeData().getNodeVisualData() == null ) {
6361 node.getNodeData().setNodeVisualData( new NodeVisualData() );
6363 node.getNodeData().getNodeVisualData().setFontColor( new Color( c.getRed(), c.getGreen(), c.getBlue() ) );
6366 final private static void drawString( final String str, final float x, final float y, final Graphics2D g ) {
6367 g.drawString( str, x, y );
6370 final private void drawStringX( final String str, final float x, final float y, final Graphics2D g ) {
6373 if ( getAttributedStringMap() == null /*&& getAttributedStringMap().containsKey(str) */ ) {
6374 final AttributedString as = new AttributedString( str );
6375 //Font plainFont = new Font("Times New Roman", Font.PLAIN, 24);
6376 as.addAttribute( TextAttribute.FONT, g.getFont() );
6377 as.addAttribute( TextAttribute.UNDERLINE, TextAttribute.UNDERLINE_ON, 1, 3 );
6378 as.addAttribute( TextAttribute.SUPERSCRIPT, TextAttribute.SUPERSCRIPT_SUPER, 3, 4 );
6379 as.addAttribute( TextAttribute.FOREGROUND, Color.BLUE, 1, 2 );
6380 as.addAttribute( TextAttribute.FOREGROUND, Color.PINK, 3, 5 );
6381 as.addAttribute( TextAttribute.STRIKETHROUGH, TextAttribute.STRIKETHROUGH_ON, 2, 4 );
6382 g.drawString( as.getIterator(), x, y );
6385 g.drawString( str, x, y );
6389 private final Map<String, AttributedString> getAttributedStringMap() {
6390 return _attributed_string_map;
6393 private final void setAttributedStringMap( final Map<String, AttributedString> attributed_string_map ) {
6394 _attributed_string_map = attributed_string_map;
6397 final private static boolean plusPressed( final int key_code ) {
6398 return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
6399 || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON )
6400 || ( key_code == KeyEvent.VK_1 ) );
6403 public void decreaseDepthCollapseLevel() {
6404 if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) {
6405 if ( _depth_collapse_level <= 1 ) {
6406 _depth_collapse_level = PhylogenyMethods.calculateMaxDepth( _phylogeny );
6410 --_depth_collapse_level;
6411 PhylogenyMethods.collapseToDepth( _phylogeny, _depth_collapse_level );
6416 public void increaseDepthCollapseLevel() {
6417 if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) {
6418 final int max = PhylogenyMethods.calculateMaxDepth( _phylogeny );
6419 if ( _depth_collapse_level >= max ) {
6420 _depth_collapse_level = 1;
6423 ++_depth_collapse_level;
6425 PhylogenyMethods.collapseToDepth( _phylogeny, _depth_collapse_level );
6429 public void decreaseRankCollapseLevel() {
6430 if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) {
6431 final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( _phylogeny );
6432 if ( ranks.length > 1 ) {
6433 if ( _rank_collapse_level <= 0 ) {
6434 _rank_collapse_level = ranks.length - 1;
6438 --_rank_collapse_level;
6439 PhylogenyMethods.collapseToRank( _phylogeny,
6440 mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) );
6446 public void increaseRankCollapseLevel() {
6447 if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) {
6448 final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( _phylogeny );
6449 if ( ranks.length > 1 ) {
6450 if ( _rank_collapse_level >= ( ranks.length - 1 ) ) {
6451 _rank_collapse_level = 0;
6452 PhylogenyMethods.collapseToRank( _phylogeny,
6453 mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) );
6455 else if ( _rank_collapse_level == ( ranks.length - 2 ) ) {
6456 ++_rank_collapse_level;
6460 ++_rank_collapse_level;
6461 PhylogenyMethods.collapseToRank( _phylogeny,
6462 mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) );
6468 private final static int mapToAbsoluteRankLevel( final String present_ranks_sorted[],
6469 final int rank_collapse_level ) {
6470 final String rank_str = present_ranks_sorted[ rank_collapse_level ];
6471 if ( !TaxonomyUtil.RANK_TO_INT.containsKey( rank_str ) ) {
6472 throw new IllegalStateException( "unexpected exception: cannot find rank " + rank_str );
6474 return TaxonomyUtil.RANK_TO_INT.get( rank_str );
6477 private final void uncollapseAll() {
6478 final PhylogenyNodeIterator it = new PreorderTreeIterator( _phylogeny );
6479 while ( it.hasNext() ) {
6480 it.next().setCollapse( false );
6484 final int resetDepthCollapseDepthValue() {
6485 return _depth_collapse_level = -1;
6488 final int getDepthCollapseDepthValue() {
6489 return _depth_collapse_level;
6492 final void setDepthCollapseDepthValue( final int depth_collapse_level ) {
6493 _depth_collapse_level = depth_collapse_level;
6496 final int resetRankCollapseRankValue() {
6497 return _rank_collapse_level = -1;
6500 final int getRankCollapseRankValue() {
6501 return _rank_collapse_level;
6504 final void setRankCollapseRankValue( final int rank_collapse_level ) {
6505 _rank_collapse_level = rank_collapse_level;