2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import jalview.analysis.*;
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23 import jalview.datamodel.*;
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25 import jalview.schemes.*;
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27 import jalview.util.*;
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30 import java.awt.event.*;
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31 import java.awt.print.*;
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35 import javax.swing.*;
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42 * @version $Revision$
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44 public class TreeCanvas extends JPanel implements MouseListener, Runnable,
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47 /** DOCUMENT ME!! */
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48 public static final String PLACEHOLDER = " * ";
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50 JScrollPane scrollPane;
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54 boolean fitToWindow = true;
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55 boolean showDistances = false;
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56 boolean showBootstrap = false;
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57 boolean markPlaceholders = false;
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62 int labelLength = -1;
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64 //RubberbandRectangle rubberband;
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66 Hashtable nameHash = new Hashtable();
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67 Hashtable nodeHash = new Hashtable();
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70 * Creates a new TreeCanvas object.
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72 * @param av DOCUMENT ME!
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73 * @param tree DOCUMENT ME!
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74 * @param scroller DOCUMENT ME!
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75 * @param label DOCUMENT ME!
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77 public TreeCanvas(AlignViewport av, JScrollPane scroller)
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80 scrollPane = scroller;
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81 addMouseListener(this);
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82 PaintRefresher.Register(this, av.alignment);
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89 * @param sequence DOCUMENT ME!
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91 public void TreeSelectionChanged(Sequence sequence)
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93 SequenceGroup selected = av.getSelectionGroup();
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95 if (selected == null)
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97 selected = new SequenceGroup();
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98 av.setSelectionGroup(selected);
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101 selected.setEndRes(av.alignment.getWidth()-1);
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102 selected.addOrRemove(sequence, true);
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104 PaintRefresher.Refresh(this, av.alignment);
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111 * @param tree DOCUMENT ME!
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113 public void setTree(NJTree tree)
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116 tree.findHeight(tree.getTopNode());
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118 // Now have to calculate longest name based on the leaves
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119 Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
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120 boolean has_placeholders = false;
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123 for (int i = 0; i < leaves.size(); i++)
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125 SequenceNode lf = (SequenceNode) leaves.elementAt(i);
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127 if (lf.isPlaceholder())
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129 has_placeholders = true;
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132 if (longestName.length() < ( (Sequence) lf.element()).getName()
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135 longestName = TreeCanvas.PLACEHOLDER +
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136 ( (Sequence) lf.element()).getName();
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140 setMarkPlaceholders(has_placeholders);
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146 * @param g DOCUMENT ME!
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147 * @param node DOCUMENT ME!
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148 * @param chunk DOCUMENT ME!
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149 * @param scale DOCUMENT ME!
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150 * @param width DOCUMENT ME!
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151 * @param offx DOCUMENT ME!
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152 * @param offy DOCUMENT ME!
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154 public void drawNode(Graphics g, SequenceNode node, float chunk,
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155 float scale, int width, int offx, int offy)
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162 if ((node.left() == null) && (node.right() == null))
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164 // Drawing leaf node
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165 float height = node.height;
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166 float dist = node.dist;
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168 int xstart = (int) ((height - dist) * scale) + offx;
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169 int xend = (int) (height * scale) + offx;
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171 int ypos = (int) (node.ycount * chunk) + offy;
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173 if (node.element() instanceof SequenceI)
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175 if (((SequenceI) ((SequenceNode) node).element()).getColor() == Color.white)
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177 g.setColor(Color.black);
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181 g.setColor(((SequenceI) ((SequenceNode) node).element()).getColor()
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187 g.setColor(Color.black);
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190 // Draw horizontal line
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191 g.drawLine(xstart, ypos, xend, ypos);
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193 String nodeLabel = "";
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195 if (showDistances && (node.dist > 0))
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197 nodeLabel = new Format("%5.2f").form(node.dist);
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204 nodeLabel = nodeLabel + " : ";
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207 nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
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210 if (!nodeLabel.equals(""))
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212 g.drawString(nodeLabel, xstart, ypos - 10);
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215 String name = (markPlaceholders && node.isPlaceholder())
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216 ? (PLACEHOLDER + node.getName()) : node.getName();
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217 FontMetrics fm = g.getFontMetrics(font);
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218 int charWidth = fm.stringWidth(name) + 3;
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219 int charHeight = fm.getHeight();
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221 Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,
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222 charWidth, charHeight);
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224 nameHash.put((SequenceI) node.element(), rect);
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226 // Colour selected leaves differently
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227 SequenceGroup selected = av.getSelectionGroup();
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229 if ((selected != null) &&
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230 selected.sequences.contains((SequenceI) node.element()))
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232 g.setColor(Color.gray);
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234 g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,
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236 g.setColor(Color.white);
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239 g.drawString(name, xend + 10, ypos);
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240 g.setColor(Color.black);
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244 drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
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246 drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
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249 float height = node.height;
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250 float dist = node.dist;
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252 int xstart = (int) ((height - dist) * scale) + offx;
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253 int xend = (int) (height * scale) + offx;
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254 int ypos = (int) (node.ycount * chunk) + offy;
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256 g.setColor(((SequenceNode) node).color.darker());
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258 // Draw horizontal line
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259 g.drawLine(xstart, ypos, xend, ypos);
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260 g.fillRect(xend - 2, ypos - 2, 4, 4);
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262 int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) +
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264 int yend = (int) (((SequenceNode) node.right()).ycount * chunk) +
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267 Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
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268 nodeHash.put(node, pos);
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270 g.drawLine((int) (height * scale) + offx, ystart,
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271 (int) (height * scale) + offx, yend);
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273 if (showDistances && (node.dist > 0))
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275 g.drawString(new Format("%5.2f").form(node.dist), xstart,
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284 * @param x DOCUMENT ME!
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285 * @param y DOCUMENT ME!
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287 * @return DOCUMENT ME!
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289 public Object findElement(int x, int y)
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291 Enumeration keys = nameHash.keys();
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293 while (keys.hasMoreElements())
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295 Object ob = keys.nextElement();
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296 Rectangle rect = (Rectangle) nameHash.get(ob);
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298 if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
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299 (y <= (rect.y + rect.height)))
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305 keys = nodeHash.keys();
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307 while (keys.hasMoreElements())
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309 Object ob = keys.nextElement();
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310 Rectangle rect = (Rectangle) nodeHash.get(ob);
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312 if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
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313 (y <= (rect.y + rect.height)))
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325 * @param pickBox DOCUMENT ME!
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327 public void pickNodes(Rectangle pickBox)
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329 int width = getWidth();
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330 int height = getHeight();
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332 SequenceNode top = tree.getTopNode();
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334 float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();
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336 if (top.count == 0)
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338 top.count = ((SequenceNode) top.left()).count +
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339 ((SequenceNode) top.right()).count;
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342 float chunk = (float) (height - (offy * 2)) / top.count;
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344 pickNode(pickBox, top, chunk, wscale, width, offx, offy);
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350 * @param pickBox DOCUMENT ME!
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351 * @param node DOCUMENT ME!
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352 * @param chunk DOCUMENT ME!
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353 * @param scale DOCUMENT ME!
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354 * @param width DOCUMENT ME!
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355 * @param offx DOCUMENT ME!
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356 * @param offy DOCUMENT ME!
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358 public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
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359 float scale, int width, int offx, int offy)
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366 if ((node.left() == null) && (node.right() == null))
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368 float height = node.height;
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369 float dist = node.dist;
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371 int xstart = (int) ((height - dist) * scale) + offx;
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372 int xend = (int) (height * scale) + offx;
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374 int ypos = (int) (node.ycount * chunk) + offy;
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376 if (pickBox.contains(new Point(xend, ypos)))
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378 if (node.element() instanceof SequenceI)
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380 SequenceI seq = (SequenceI) node.element();
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381 SequenceGroup sg = av.getSelectionGroup();
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385 sg.addOrRemove(seq, true);
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392 pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
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394 pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
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402 * @param node DOCUMENT ME!
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403 * @param c DOCUMENT ME!
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405 public void setColor(SequenceNode node, Color c)
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412 if ((node.left() == null) && (node.right() == null))
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416 if (node.element() instanceof SequenceI)
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418 ((SequenceI) node.element()).setColor(c);
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424 setColor((SequenceNode) node.left(), c);
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425 setColor((SequenceNode) node.right(), c);
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432 void startPrinting()
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434 Thread thread = new Thread(this);
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438 // put printing in a thread to avoid painting problems
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441 PrinterJob printJob = PrinterJob.getPrinterJob();
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442 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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444 printJob.setPrintable(this, pf);
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446 if (printJob.printDialog())
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452 catch (Exception PrintException)
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454 PrintException.printStackTrace();
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462 * @param pg DOCUMENT ME!
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463 * @param pf DOCUMENT ME!
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464 * @param pi DOCUMENT ME!
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466 * @return DOCUMENT ME!
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468 * @throws PrinterException DOCUMENT ME!
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470 public int print(Graphics pg, PageFormat pf, int pi)
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471 throws PrinterException
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474 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
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476 int pwidth = (int) pf.getImageableWidth();
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477 int pheight = (int) pf.getImageableHeight();
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479 int noPages = getHeight() / pheight;
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483 return Printable.NO_SUCH_PAGE;
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486 if (pwidth > getWidth())
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488 pwidth = getWidth();
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493 if (pheight > getHeight())
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495 pheight = getHeight();
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502 FontMetrics fm = pg.getFontMetrics(font);
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503 int height = fm.getHeight() * nameHash.size();
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504 pg.translate(0, -pi * pheight);
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505 pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);
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507 // translate number of pages,
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508 // height is screen size as this is the
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509 // non overlapping text size
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513 draw(pg, pwidth, pheight);
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515 return Printable.PAGE_EXISTS;
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521 * @param g DOCUMENT ME!
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523 public void paintComponent(Graphics g)
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525 super.paintComponent(g);
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528 g.setFont(new Font("Verdana", Font.PLAIN, 18));
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529 g.drawString("Calculating tree....", 20, getHeight()/2);
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534 font = new Font("Verdana", Font.PLAIN, fontSize);
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537 FontMetrics fm = g.getFontMetrics(font);
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539 if (nameHash.size() == 0)
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546 (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +
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549 draw(g, scrollPane.getWidth(), scrollPane.getHeight());
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550 setPreferredSize(null);
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554 setPreferredSize(new Dimension(scrollPane.getWidth(),
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555 fm.getHeight() * nameHash.size()));
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556 draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
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559 scrollPane.revalidate();
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566 * @return DOCUMENT ME!
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568 public int getFontSize()
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576 * @param fontSize DOCUMENT ME!
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578 public void setFontSize(int fontSize)
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580 this.fontSize = fontSize;
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587 * @param g1 DOCUMENT ME!
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588 * @param width DOCUMENT ME!
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589 * @param height DOCUMENT ME!
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591 public void draw(Graphics g1, int width, int height)
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593 Graphics2D g2 = (Graphics2D) g1;
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594 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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595 RenderingHints.VALUE_ANTIALIAS_ON);
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596 g2.setColor(Color.white);
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597 g2.fillRect(0, 0, width, height);
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599 labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
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601 float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();
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603 SequenceNode top = tree.getTopNode();
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605 if (top.count == 0)
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607 top.count = ((SequenceNode) top.left()).count +
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608 ((SequenceNode) top.right()).count;
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611 float chunk = (float) (height - (offy * 2)) / top.count;
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613 drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
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615 if (threshold != 0)
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617 if (av.getCurrentTree() == tree)
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619 g2.setColor(Color.red);
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623 g2.setColor(Color.gray);
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626 int x = (int) ((threshold * (float) (getWidth() - labelLength -
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627 (2 * offx))) + offx);
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629 g2.drawLine(x, 0, x, getHeight());
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636 * @param e DOCUMENT ME!
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638 public void mouseReleased(MouseEvent e)
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645 * @param e DOCUMENT ME!
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647 public void mouseEntered(MouseEvent e)
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654 * @param e DOCUMENT ME!
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656 public void mouseExited(MouseEvent e)
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663 * @param e DOCUMENT ME!
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665 public void mouseClicked(MouseEvent e)
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672 * @param e DOCUMENT ME!
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674 public void mousePressed(MouseEvent e)
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676 av.setCurrentTree(tree);
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681 Object ob = findElement(x, y);
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683 if (ob instanceof SequenceI)
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685 TreeSelectionChanged((Sequence) ob);
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690 else if (ob instanceof SequenceNode)
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692 SequenceNode tmpnode = (SequenceNode) ob;
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693 tree.swapNodes(tmpnode);
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694 tree.reCount(tree.getTopNode());
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695 tree.findHeight(tree.getTopNode());
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700 if (tree.getMaxHeight() != 0)
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702 threshold = (float) (x - offx) / (float) (getWidth() -
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703 labelLength - (2 * offx));
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705 tree.getGroups().removeAllElements();
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706 tree.groupNodes(tree.getTopNode(), threshold);
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707 setColor(tree.getTopNode(), Color.black);
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709 av.setSelectionGroup(null);
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710 av.alignment.deleteAllGroups();
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712 for (int i = 0; i < tree.getGroups().size(); i++)
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714 Color col = new Color((int) (Math.random() * 255),
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715 (int) (Math.random() * 255),
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716 (int) (Math.random() * 255));
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717 setColor((SequenceNode) tree.getGroups().elementAt(i),
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720 Vector l = tree.findLeaves((SequenceNode) tree.getGroups()
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724 Vector sequences = new Vector();
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726 for (int j = 0; j < l.size(); j++)
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728 SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)).element();
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730 if (!sequences.contains(s1))
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732 sequences.addElement(s1);
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736 ColourSchemeI cs = null;
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738 if (av.getGlobalColourScheme() != null)
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740 if (av.getGlobalColourScheme() instanceof UserColourScheme)
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742 cs = new UserColourScheme(
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743 ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
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747 cs = ColourSchemeProperty.getColour(sequences,
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748 av.alignment.getWidth(),
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749 ColourSchemeProperty.getColourName(
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750 av.getGlobalColourScheme()));
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752 cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
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753 av.getIgnoreGapsConsensus());
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757 SequenceGroup sg = new SequenceGroup(sequences,
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758 "TreeGroup", cs, true, true, false, 0,
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759 av.alignment.getWidth());
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762 if ( av.getGlobalColourScheme()!=null
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763 && av.getGlobalColourScheme().conservationApplied())
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765 Conservation c = new Conservation("Group",
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766 ResidueProperties.propHash, 3, sg.sequences,
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767 sg.getStartRes(), sg.getEndRes());
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770 c.verdict(false, av.ConsPercGaps);
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771 sg.cs.setConservation(c);
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774 av.alignment.addGroup(sg);
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779 PaintRefresher.Refresh(this, av.alignment);
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786 * @param state DOCUMENT ME!
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788 public void setShowDistances(boolean state)
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790 this.showDistances = state;
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797 * @param state DOCUMENT ME!
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799 public void setShowBootstrap(boolean state)
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801 this.showBootstrap = state;
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808 * @param state DOCUMENT ME!
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810 public void setMarkPlaceholders(boolean state)
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812 this.markPlaceholders = state;
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