2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.appletgui;
23 import java.awt.event.*;
25 import jalview.analysis.*;
26 import jalview.datamodel.*;
27 import jalview.schemes.*;
28 import jalview.util.*;
30 public class TreeCanvas extends Panel implements MouseListener,
35 ScrollPane scrollPane;
39 public static final String PLACEHOLDER = " * ";
43 boolean fitToWindow = true;
45 boolean showDistances = false;
47 boolean showBootstrap = false;
49 boolean markPlaceholders = false;
61 Hashtable nameHash = new Hashtable();
63 Hashtable nodeHash = new Hashtable();
65 SequenceNode highlightNode;
68 public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
73 scrollPane = scroller;
74 addMouseListener(this);
75 addMouseMotionListener(this);
78 PaintRefresher.Register(this, av.getSequenceSetId());
81 public void treeSelectionChanged(SequenceI sequence)
83 SequenceGroup selected = av.getSelectionGroup();
86 selected = new SequenceGroup();
87 av.setSelectionGroup(selected);
90 selected.setEndRes(av.getAlignment().getWidth() - 1);
91 selected.addOrRemove(sequence, true);
94 public void setTree(NJTree tree)
97 tree.findHeight(tree.getTopNode());
99 // Now have to calculate longest name based on the leaves
100 Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
101 boolean has_placeholders = false;
104 for (int i = 0; i < leaves.size(); i++)
106 SequenceNode lf = (SequenceNode) leaves.elementAt(i);
108 if (lf.isPlaceholder())
110 has_placeholders = true;
113 if (longestName.length() < ((Sequence) lf.element()).getName()
116 longestName = TreeCanvas.PLACEHOLDER
117 + ((Sequence) lf.element()).getName();
121 setMarkPlaceholders(has_placeholders);
124 public void drawNode(Graphics g, SequenceNode node, float chunk,
125 float scale, int width, int offx, int offy)
132 if (node.left() == null && node.right() == null)
136 float height = node.height;
137 float dist = node.dist;
139 int xstart = (int) ((height - dist) * scale) + offx;
140 int xend = (int) (height * scale) + offx;
142 int ypos = (int) (node.ycount * chunk) + offy;
144 if (node.element() instanceof SequenceI)
146 SequenceI seq = (SequenceI) node.element();
148 if (av.getSequenceColour(seq) == Color.white)
150 g.setColor(Color.black);
154 g.setColor(av.getSequenceColour(seq).darker());
160 g.setColor(Color.black);
163 // Draw horizontal line
164 g.drawLine(xstart, ypos, xend, ypos);
166 String nodeLabel = "";
167 if (showDistances && node.dist > 0)
169 nodeLabel = new Format("%-.2f").form(node.dist);
173 int btstrap = node.getBootstrap();
178 nodeLabel = nodeLabel + " : ";
180 nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
183 if (!nodeLabel.equals(""))
185 g.drawString(nodeLabel, xstart + 2, ypos - 2);
188 String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
189 .getName()) : node.getName();
190 FontMetrics fm = g.getFontMetrics(font);
191 int charWidth = fm.stringWidth(name) + 3;
192 int charHeight = fm.getHeight();
194 Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
195 charWidth, charHeight);
197 nameHash.put(node.element(), rect);
199 // Colour selected leaves differently
200 SequenceGroup selected = av.getSelectionGroup();
202 && selected.getSequences(null).contains(
205 g.setColor(Color.gray);
207 g.fillRect(xend + 10, ypos - charHeight + 3, charWidth, charHeight);
208 g.setColor(Color.white);
210 g.drawString(name, xend + 10, ypos);
211 g.setColor(Color.black);
215 drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
217 drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
220 float height = node.height;
221 float dist = node.dist;
223 int xstart = (int) ((height - dist) * scale) + offx;
224 int xend = (int) (height * scale) + offx;
225 int ypos = (int) (node.ycount * chunk) + offy;
227 g.setColor(node.color.darker());
229 // Draw horizontal line
230 g.drawLine(xstart, ypos, xend, ypos);
231 if (node == highlightNode)
233 g.fillRect(xend - 3, ypos - 3, 6, 6);
237 g.fillRect(xend - 2, ypos - 2, 4, 4);
240 int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
242 int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
245 Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
246 nodeHash.put(node, pos);
248 g.drawLine((int) (height * scale) + offx, ystart,
249 (int) (height * scale) + offx, yend);
251 String nodeLabel = "";
253 if (showDistances && (node.dist > 0))
255 nodeLabel = new Format("%-.2f").form(node.dist);
260 int btstrap = node.getBootstrap();
265 nodeLabel = nodeLabel + " : ";
267 nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
271 if (!nodeLabel.equals(""))
273 g.drawString(nodeLabel, xstart + 2, ypos - 2);
279 public Object findElement(int x, int y)
281 Enumeration keys = nameHash.keys();
283 while (keys.hasMoreElements())
285 Object ob = keys.nextElement();
286 Rectangle rect = (Rectangle) nameHash.get(ob);
288 if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y
289 && y <= (rect.y + rect.height))
294 keys = nodeHash.keys();
296 while (keys.hasMoreElements())
298 Object ob = keys.nextElement();
299 Rectangle rect = (Rectangle) nodeHash.get(ob);
301 if (x >= rect.x && x <= (rect.x + rect.width) && y >= rect.y
302 && y <= (rect.y + rect.height))
311 public void pickNodes(Rectangle pickBox)
313 int width = getSize().width;
314 int height = getSize().height;
316 SequenceNode top = tree.getTopNode();
318 float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
321 top.count = ((SequenceNode) top.left()).count
322 + ((SequenceNode) top.right()).count;
324 float chunk = (float) (height - offy) / top.count;
326 pickNode(pickBox, top, chunk, wscale, width, offx, offy);
329 public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
330 float scale, int width, int offx, int offy)
337 if (node.left() == null && node.right() == null)
339 float height = node.height;
340 // float dist = node.dist;
342 // int xstart = (int) ( (height - dist) * scale) + offx;
343 int xend = (int) (height * scale) + offx;
345 int ypos = (int) (node.ycount * chunk) + offy;
347 if (pickBox.contains(new Point(xend, ypos)))
349 if (node.element() instanceof SequenceI)
351 SequenceI seq = (SequenceI) node.element();
352 SequenceGroup sg = av.getSelectionGroup();
355 sg.addOrRemove(seq, true);
362 pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
364 pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
369 public void setColor(SequenceNode node, Color c)
376 if (node.left() == null && node.right() == null)
380 if (node.element() instanceof SequenceI)
382 av.setSequenceColour((SequenceI) node.element(), c);
388 setColor((SequenceNode) node.left(), c);
389 setColor((SequenceNode) node.right(), c);
394 public void update(Graphics g)
400 public void paint(Graphics g)
407 if (nameHash.size() == 0)
412 int width = scrollPane.getSize().width;
413 int height = scrollPane.getSize().height;
416 height = g.getFontMetrics(font).getHeight() * nameHash.size();
419 if (getSize().width > width)
421 setSize(new Dimension(width, height));
422 scrollPane.validate();
426 setSize(new Dimension(width, height));
429 draw(g, width, height);
433 public void draw(Graphics g, int width, int height)
435 offy = font.getSize() + 10;
437 g.setColor(Color.white);
438 g.fillRect(0, 0, width, height);
440 labelLength = g.getFontMetrics(font).stringWidth(longestName) + 20; // 20
445 float wscale = (width - labelLength - offx * 2)
446 / tree.getMaxHeight();
448 SequenceNode top = tree.getTopNode();
452 top.count = ((SequenceNode) top.left()).count
453 + ((SequenceNode) top.right()).count;
455 float chunk = (float) (height - offy) / top.count;
457 drawNode(g, tree.getTopNode(), chunk, wscale, width, offx, offy);
461 if (av.getCurrentTree() == tree)
463 g.setColor(Color.red);
467 g.setColor(Color.gray);
470 int x = (int) (threshold
471 * (getSize().width - labelLength - 2 * offx) + offx);
473 g.drawLine(x, 0, x, getSize().height);
479 public void mouseReleased(MouseEvent e)
484 public void mouseEntered(MouseEvent e)
489 public void mouseExited(MouseEvent e)
494 public void mouseClicked(MouseEvent evt)
496 if (highlightNode != null)
498 if (evt.getClickCount() > 1)
500 tree.swapNodes(highlightNode);
501 tree.reCount(tree.getTopNode());
502 tree.findHeight(tree.getTopNode());
506 Vector leaves = new Vector();
507 tree.findLeaves(highlightNode, leaves);
509 for (int i = 0; i < leaves.size(); i++)
511 SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
513 treeSelectionChanged(seq);
517 PaintRefresher.Refresh(this, av.getSequenceSetId());
524 public void mouseDragged(MouseEvent ect)
529 public void mouseMoved(MouseEvent evt)
531 av.setCurrentTree(tree);
533 Object ob = findElement(evt.getX(), evt.getY());
535 if (ob instanceof SequenceNode)
537 highlightNode = (SequenceNode) ob;
542 if (highlightNode != null)
544 highlightNode = null;
551 public void mousePressed(MouseEvent e)
553 av.setCurrentTree(tree);
558 Object ob = findElement(x, y);
560 if (ob instanceof SequenceI)
562 treeSelectionChanged((Sequence) ob);
563 PaintRefresher.Refresh(this, av.getSequenceSetId());
568 else if (!(ob instanceof SequenceNode))
572 if (tree.getMaxHeight() != 0)
574 threshold = (float) (x - offx)
575 / (float) (getSize().width - labelLength - 2 * offx);
577 tree.getGroups().removeAllElements();
578 tree.groupNodes(tree.getTopNode(), threshold);
579 setColor(tree.getTopNode(), Color.black);
581 av.setSelectionGroup(null);
582 av.getAlignment().deleteAllGroups();
583 av.sequenceColours = null;
590 PaintRefresher.Refresh(this, av.getSequenceSetId());
597 for (int i = 0; i < tree.getGroups().size(); i++)
600 Color col = new Color((int) (Math.random() * 255),
601 (int) (Math.random() * 255), (int) (Math.random() * 255));
602 setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
604 Vector l = tree.findLeaves(
605 (SequenceNode) tree.getGroups().elementAt(i), new Vector());
607 Vector sequences = new Vector();
608 for (int j = 0; j < l.size(); j++)
610 SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
612 if (!sequences.contains(s1))
614 sequences.addElement(s1);
618 ColourSchemeI cs = null;
620 SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
621 false, 0, av.getAlignment().getWidth() - 1);
623 if (av.getGlobalColourScheme() != null)
625 if (av.getGlobalColourScheme() instanceof UserColourScheme)
627 cs = new UserColourScheme(
628 ((UserColourScheme) av.getGlobalColourScheme())
634 cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty.getColourName(av
635 .getGlobalColourScheme()));
637 // cs is null if shading is an annotationColourGradient
640 cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
641 av.getIgnoreGapsConsensus());
644 // TODO: cs used to be initialized with a sequence collection and recalcConservation called automatically
645 // instead we set it manually - recalc called after updateAnnotation
648 sg.setName("JTreeGroup:" + sg.hashCode());
650 if (av.getGlobalColourScheme() != null
651 && av.getGlobalColourScheme().conservationApplied())
653 Conservation c = new Conservation("Group",
654 ResidueProperties.propHash, 3, sg.getSequences(null),
655 sg.getStartRes(), sg.getEndRes());
658 c.verdict(false, av.getConsPercGaps());
659 cs.setConservation(c);
665 av.getAlignment().addGroup(sg);
668 ap.updateAnnotation();
672 public void setShowDistances(boolean state)
674 this.showDistances = state;
678 public void setShowBootstrap(boolean state)
680 this.showBootstrap = state;
684 public void setMarkPlaceholders(boolean state)
686 this.markPlaceholders = state;