2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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45 Printable, MouseMotionListener
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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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55 boolean fitToWindow = true;
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56 boolean showDistances = false;
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57 boolean showBootstrap = false;
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58 boolean markPlaceholders = false;
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63 int labelLength = -1;
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65 Hashtable nameHash = new Hashtable();
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66 Hashtable nodeHash = new Hashtable();
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67 SequenceNode highlightNode;
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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(AlignmentPanel ap, JScrollPane scroller)
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81 font = av.getFont();
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82 scrollPane = scroller;
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83 addMouseListener(this);
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84 addMouseMotionListener(this);
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85 PaintRefresher.Register(this, ap.av.getSequenceSetId());
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86 ToolTipManager.sharedInstance().registerComponent(this);
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93 * @param sequence DOCUMENT ME!
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95 public void treeSelectionChanged(SequenceI sequence)
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97 SequenceGroup selected = av.getSelectionGroup();
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99 if (selected == null)
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101 selected = new SequenceGroup();
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102 av.setSelectionGroup(selected);
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105 selected.setEndRes(av.alignment.getWidth()-1);
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106 selected.addOrRemove(sequence, true);
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112 * @param tree DOCUMENT ME!
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114 public void setTree(NJTree tree)
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117 tree.findHeight(tree.getTopNode());
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119 // Now have to calculate longest name based on the leaves
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120 Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
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121 boolean has_placeholders = false;
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124 for (int i = 0; i < leaves.size(); i++)
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126 SequenceNode lf = (SequenceNode) leaves.elementAt(i);
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128 if (lf.isPlaceholder())
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130 has_placeholders = true;
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133 if (longestName.length() < ( (Sequence) lf.element()).getName()
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136 longestName = TreeCanvas.PLACEHOLDER +
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137 ( (Sequence) lf.element()).getName();
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141 setMarkPlaceholders(has_placeholders);
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147 * @param g DOCUMENT ME!
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148 * @param node DOCUMENT ME!
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149 * @param chunk DOCUMENT ME!
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150 * @param scale DOCUMENT ME!
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151 * @param width DOCUMENT ME!
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152 * @param offx DOCUMENT ME!
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153 * @param offy DOCUMENT ME!
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155 public void drawNode(Graphics g, SequenceNode node, float chunk,
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156 float scale, int width, int offx, int offy)
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163 if ((node.left() == null) && (node.right() == null))
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165 // Drawing leaf node
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166 float height = node.height;
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167 float dist = node.dist;
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169 int xstart = (int) ((height - dist) * scale) + offx;
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170 int xend = (int) (height * scale) + offx;
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172 int ypos = (int) (node.ycount * chunk) + offy;
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174 if (node.element() instanceof SequenceI)
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176 SequenceI seq = (SequenceI)((SequenceNode) node).element();
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178 if (av.getSequenceColour(seq) == Color.white)
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180 g.setColor(Color.black);
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184 g.setColor(av.getSequenceColour(seq).darker());
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189 g.setColor(Color.black);
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192 // Draw horizontal line
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193 g.drawLine(xstart, ypos, xend, ypos);
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195 String nodeLabel = "";
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197 if (showDistances && (node.dist > 0))
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199 nodeLabel = new Format("%-.2f").form(node.dist);
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206 nodeLabel = nodeLabel + " : ";
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209 nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
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212 if (!nodeLabel.equals(""))
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214 g.drawString(nodeLabel, xstart+2, ypos - 2);
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217 String name = (markPlaceholders && node.isPlaceholder())
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218 ? (PLACEHOLDER + node.getName()) : node.getName();
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220 int charWidth = fm.stringWidth(name) + 3;
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221 int charHeight = font.getSize();
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223 Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,
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224 charWidth, charHeight);
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226 nameHash.put((SequenceI) node.element(), rect);
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228 // Colour selected leaves differently
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229 SequenceGroup selected = av.getSelectionGroup();
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231 if ((selected != null) &&
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232 selected.getSequences(false).contains((SequenceI) node.element()))
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234 g.setColor(Color.gray);
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236 g.fillRect(xend + 10, ypos-charHeight/2, charWidth,
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238 g.setColor(Color.white);
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241 g.drawString(name, xend + 10, ypos+fm.getDescent());
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242 g.setColor(Color.black);
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246 drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
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248 drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
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251 float height = node.height;
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252 float dist = node.dist;
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254 int xstart = (int) ((height - dist) * scale) + offx;
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255 int xend = (int) (height * scale) + offx;
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256 int ypos = (int) (node.ycount * chunk) + offy;
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258 g.setColor(((SequenceNode) node).color.darker());
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260 // Draw horizontal line
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261 g.drawLine(xstart, ypos, xend, ypos);
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262 if (node == highlightNode)
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263 g.fillRect(xend - 3, ypos - 3, 6, 6);
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265 g.fillRect(xend - 2, ypos - 2, 4, 4);
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267 int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) +
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269 int yend = (int) (((SequenceNode) node.right()).ycount * chunk) +
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272 Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
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273 nodeHash.put(node, pos);
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275 g.drawLine((int) (height * scale) + offx, ystart,
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276 (int) (height * scale) + offx, yend);
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278 if (showDistances && (node.dist > 0))
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280 g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2,
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289 * @param x DOCUMENT ME!
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290 * @param y DOCUMENT ME!
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292 * @return DOCUMENT ME!
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294 public Object findElement(int x, int y)
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296 Enumeration keys = nameHash.keys();
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298 while (keys.hasMoreElements())
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300 Object ob = keys.nextElement();
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301 Rectangle rect = (Rectangle) nameHash.get(ob);
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303 if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
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304 (y <= (rect.y + rect.height)))
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310 keys = nodeHash.keys();
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312 while (keys.hasMoreElements())
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314 Object ob = keys.nextElement();
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315 Rectangle rect = (Rectangle) nodeHash.get(ob);
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317 if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&
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318 (y <= (rect.y + rect.height)))
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330 * @param pickBox DOCUMENT ME!
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332 public void pickNodes(Rectangle pickBox)
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334 int width = getWidth();
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335 int height = getHeight();
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337 SequenceNode top = tree.getTopNode();
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339 float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();
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341 if (top.count == 0)
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343 top.count = ((SequenceNode) top.left()).count +
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344 ((SequenceNode) top.right()).count;
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347 float chunk = (float) (height - (offy)) / top.count;
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349 pickNode(pickBox, top, chunk, wscale, width, offx, offy);
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355 * @param pickBox DOCUMENT ME!
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356 * @param node DOCUMENT ME!
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357 * @param chunk DOCUMENT ME!
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358 * @param scale DOCUMENT ME!
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359 * @param width DOCUMENT ME!
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360 * @param offx DOCUMENT ME!
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361 * @param offy DOCUMENT ME!
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363 public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
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364 float scale, int width, int offx, int offy)
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371 if ((node.left() == null) && (node.right() == null))
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373 float height = node.height;
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374 float dist = node.dist;
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376 int xstart = (int) ((height - dist) * scale) + offx;
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377 int xend = (int) (height * scale) + offx;
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379 int ypos = (int) (node.ycount * chunk) + offy;
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381 if (pickBox.contains(new Point(xend, ypos)))
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383 if (node.element() instanceof SequenceI)
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385 SequenceI seq = (SequenceI) node.element();
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386 SequenceGroup sg = av.getSelectionGroup();
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390 sg.addOrRemove(seq, true);
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397 pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
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399 pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
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407 * @param node DOCUMENT ME!
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408 * @param c DOCUMENT ME!
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410 public void setColor(SequenceNode node, Color c)
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417 if ((node.left() == null) && (node.right() == null))
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421 if (node.element() instanceof SequenceI)
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423 av.setSequenceColour((SequenceI) node.element(), c);
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429 setColor((SequenceNode) node.left(), c);
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430 setColor((SequenceNode) node.right(), c);
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437 void startPrinting()
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439 Thread thread = new Thread(this);
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443 // put printing in a thread to avoid painting problems
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446 PrinterJob printJob = PrinterJob.getPrinterJob();
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447 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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449 printJob.setPrintable(this, pf);
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451 if (printJob.printDialog())
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457 catch (Exception PrintException)
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459 PrintException.printStackTrace();
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467 * @param pg DOCUMENT ME!
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468 * @param pf DOCUMENT ME!
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469 * @param pi DOCUMENT ME!
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471 * @return DOCUMENT ME!
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473 * @throws PrinterException DOCUMENT ME!
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475 public int print(Graphics pg, PageFormat pf, int pi)
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476 throws PrinterException
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479 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
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481 int pwidth = (int) pf.getImageableWidth();
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482 int pheight = (int) pf.getImageableHeight();
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484 int noPages = getHeight() / pheight;
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488 return Printable.NO_SUCH_PAGE;
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491 if (pwidth > getWidth())
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493 pwidth = getWidth();
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498 if (pheight > getHeight())
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500 pheight = getHeight();
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507 FontMetrics fm = pg.getFontMetrics(font);
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508 int height = fm.getHeight() * nameHash.size();
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509 pg.translate(0, -pi * pheight);
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510 pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);
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512 // translate number of pages,
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513 // height is screen size as this is the
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514 // non overlapping text size
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518 draw(pg, pwidth, pheight);
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520 return Printable.PAGE_EXISTS;
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526 * @param g DOCUMENT ME!
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528 public void paintComponent(Graphics g)
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530 super.paintComponent(g);
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535 g.drawString("Calculating tree....", 20, getHeight()/2);
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539 fm = g.getFontMetrics(font);
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541 if (nameHash.size() == 0)
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548 (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +
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551 draw(g, scrollPane.getWidth(), scrollPane.getHeight());
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552 setPreferredSize(null);
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556 setPreferredSize(new Dimension(scrollPane.getWidth(),
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557 fm.getHeight() * nameHash.size()));
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558 draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
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561 scrollPane.revalidate();
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569 * @param fontSize DOCUMENT ME!
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571 public void setFont(Font font)
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580 * @param g1 DOCUMENT ME!
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581 * @param width DOCUMENT ME!
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582 * @param height DOCUMENT ME!
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584 public void draw(Graphics g1, int width, int height)
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586 Graphics2D g2 = (Graphics2D) g1;
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587 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
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588 RenderingHints.VALUE_ANTIALIAS_ON);
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589 g2.setColor(Color.white);
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590 g2.fillRect(0, 0, width, height);
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594 offy = font.getSize()+10;
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596 fm = g2.getFontMetrics(font);
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598 labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar
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600 float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();
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602 SequenceNode top = tree.getTopNode();
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604 if (top.count == 0)
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606 top.count = ((SequenceNode) top.left()).count +
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607 ((SequenceNode) top.right()).count;
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610 float chunk = (float) (height - (offy)) / top.count;
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612 drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);
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614 if (threshold != 0)
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616 if (av.getCurrentTree() == tree)
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618 g2.setColor(Color.red);
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622 g2.setColor(Color.gray);
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625 int x = (int) ((threshold * (float) (getWidth() - labelLength -
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626 (2 * offx))) + offx);
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628 g2.drawLine(x, 0, x, getHeight());
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635 * @param e DOCUMENT ME!
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637 public void mouseReleased(MouseEvent e)
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644 * @param e DOCUMENT ME!
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646 public void mouseEntered(MouseEvent e)
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653 * @param e DOCUMENT ME!
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655 public void mouseExited(MouseEvent e)
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662 * @param e DOCUMENT ME!
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664 public void mouseClicked(MouseEvent evt)
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666 if(highlightNode!=null)
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668 if (SwingUtilities.isRightMouseButton(evt))
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670 Color col = JColorChooser.showDialog(this, "Select Background Colour",
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671 highlightNode.color);
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673 setColor(highlightNode, col);
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676 if(evt.getClickCount()>1)
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678 tree.swapNodes(highlightNode);
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679 tree.reCount(tree.getTopNode());
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680 tree.findHeight(tree.getTopNode());
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684 Vector leaves = new Vector();
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685 tree.findLeaves(highlightNode, leaves);
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687 for (int i = 0; i < leaves.size(); i++)
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690 (SequenceI) ( (SequenceNode) leaves.elementAt(i)).element();
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691 treeSelectionChanged(seq);
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695 PaintRefresher.Refresh(this, av.getSequenceSetId());
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702 public void mouseMoved(MouseEvent evt)
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704 av.setCurrentTree(tree);
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706 Object ob = findElement(evt.getX(), evt.getY());
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708 if (ob instanceof SequenceNode)
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710 highlightNode = (SequenceNode) ob;
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711 this.setToolTipText(
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712 "<html>Left click to select leaves"
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713 + "<br>Double-click to invert leaves"
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714 + "<br>Right click to change colour");
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720 if (highlightNode != null)
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722 highlightNode = null;
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723 setToolTipText(null);
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729 public void mouseDragged(MouseEvent ect)
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735 * @param e DOCUMENT ME!
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737 public void mousePressed(MouseEvent e)
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739 av.setCurrentTree(tree);
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744 Object ob = findElement(x, y);
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746 if (ob instanceof SequenceI)
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748 treeSelectionChanged( (Sequence) ob);
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749 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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753 else if( !(ob instanceof SequenceNode) )
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756 if (tree.getMaxHeight() != 0)
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758 threshold = (float) (x - offx) / (float) (getWidth() -
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759 labelLength - (2 * offx));
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761 tree.getGroups().removeAllElements();
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762 tree.groupNodes(tree.getTopNode(), threshold);
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763 setColor(tree.getTopNode(), Color.black);
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765 av.setSelectionGroup(null);
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766 av.alignment.deleteAllGroups();
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767 av.sequenceColours.clear();
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772 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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779 void colourGroups()
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781 for (int i = 0; i < tree.getGroups().size(); i++)
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783 Color col = new Color( (int) (Math.random() * 255),
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784 (int) (Math.random() * 255),
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785 (int) (Math.random() * 255));
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786 setColor( (SequenceNode) tree.getGroups().elementAt(i),
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789 Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()
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793 Vector sequences = new Vector();
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795 for (int j = 0; j < l.size(); j++)
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797 SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
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799 if (!sequences.contains(s1))
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801 sequences.addElement(s1);
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805 ColourSchemeI cs = null;
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807 if (av.getGlobalColourScheme() != null)
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809 if (av.getGlobalColourScheme() instanceof UserColourScheme)
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811 cs = new UserColourScheme(
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812 ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
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816 cs = ColourSchemeProperty.getColour(sequences,
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817 av.alignment.getWidth(),
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818 ColourSchemeProperty.
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820 av.getGlobalColourScheme()));
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822 cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
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823 av.getIgnoreGapsConsensus());
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826 SequenceGroup sg = new SequenceGroup(sequences,
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827 "TreeGroup", cs, true, true, false,
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829 av.alignment.getWidth() - 1);
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831 if (av.getGlobalColourScheme() != null
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832 && av.getGlobalColourScheme().conservationApplied())
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834 Conservation c = new Conservation("Group",
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835 ResidueProperties.propHash, 3,
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836 sg.getSequences(false),
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837 sg.getStartRes(), sg.getEndRes());
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840 c.verdict(false, av.ConsPercGaps);
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841 sg.cs.setConservation(c);
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844 av.alignment.addGroup(sg);
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852 * @param state DOCUMENT ME!
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854 public void setShowDistances(boolean state)
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856 this.showDistances = state;
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863 * @param state DOCUMENT ME!
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865 public void setShowBootstrap(boolean state)
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867 this.showBootstrap = state;
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874 * @param state DOCUMENT ME!
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876 public void setMarkPlaceholders(boolean state)
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878 this.markPlaceholders = state;
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