4 import jalview.analysis.*;
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5 import jalview.datamodel.*;
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6 import jalview.util.*;
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7 import javax.swing.*;
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9 import java.awt.event.*;
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13 public class TreeCanvas extends JPanel implements MouseListener
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16 JScrollPane scrollPane;
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22 boolean showDistances = false;
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23 boolean showBootstrap = false;
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33 //RubberbandRectangle rubberband;
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38 Hashtable nameHash = new Hashtable();
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39 Hashtable nodeHash = new Hashtable();
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41 public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, String label)
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45 selected = av.getSelection();
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46 scrollPane = scroller;
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47 addMouseListener(this);
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48 tree.findHeight(tree.getTopNode());
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49 longestName = label;
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51 PaintRefresher.Register(this);
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53 public void TreeSelectionChanged(Sequence sequence)
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55 selected = av.getSelection();
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57 if (selected.contains(sequence))
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58 selected.removeElement(sequence);
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60 selected.addElement(sequence);
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62 setSelected(selected);
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63 PaintRefresher.Refresh(this);
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68 public void setSelected(Selection selected)
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70 this.selected = selected;
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73 public void setTree(NJTree tree) {
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75 tree.findHeight(tree.getTopNode());
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78 public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
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83 if (node.left() == null && node.right() == null) {
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84 // Drawing leaf node
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86 float height = node.height;
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87 float dist = node.dist;
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89 int xstart = (int)((height-dist)*scale) + offx;
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90 int xend = (int)(height*scale) + offx;
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92 int ypos = (int)(node.ycount * chunk) + offy;
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94 if (node.element() instanceof SequenceI)
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96 if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() == Color.white)
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98 g.setColor(Color.black);
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101 g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().
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106 g.setColor(Color.black);
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109 // Draw horizontal line
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110 g.drawLine(xstart,ypos,xend,ypos);
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112 String nodeLabel = "";
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113 if (showDistances && node.dist > 0) {
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114 nodeLabel = new Format("%5.2f").form(node.dist);
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116 if (showBootstrap) {
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117 if (showDistances) {
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118 nodeLabel = nodeLabel + " : ";
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120 nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());
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122 if (! nodeLabel.equals("")) {
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123 g.drawString(nodeLabel,xstart,ypos - 10);
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126 // Colour selected leaves differently
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127 String name = node.getName();
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128 FontMetrics fm = g.getFontMetrics(font);
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129 int charWidth = fm.stringWidth(node.getName()) + 3;
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130 int charHeight = fm.getHeight();
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132 Rectangle rect = new Rectangle(xend+20,ypos-charHeight,
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133 charWidth,charHeight);
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135 nameHash.put((SequenceI)node.element(),rect);
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137 if (selected.contains((SequenceI)node.element())) {
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138 g.setColor(Color.gray);
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140 g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);
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141 g.setColor(Color.white);
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143 g.drawString(node.getName(),xend+10,ypos);
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144 g.setColor(Color.black);
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146 drawNode(g,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
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147 drawNode(g,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
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149 float height = node.height;
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150 float dist = node.dist;
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152 int xstart = (int)((height-dist)*scale) + offx;
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153 int xend = (int)(height *scale) + offx;
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154 int ypos = (int)(node.ycount *chunk) + offy;
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156 g.setColor(((SequenceNode)node).color.darker());
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158 // Draw horizontal line
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159 g.drawLine(xstart,ypos,xend,ypos);
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160 g.fillRect(xend-2, ypos-2, 4,4);
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162 int ystart = (int)(((SequenceNode)node.left()) .ycount * chunk) + offy;
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163 int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;
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165 Rectangle pos = new Rectangle(xend-2,ypos-2,5,5);
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166 nodeHash.put(node,pos);
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168 g.drawLine((int)(height*scale) + offx, ystart,
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169 (int)(height*scale) + offx, yend);
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171 if (showDistances && node.dist > 0) {
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172 g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
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177 public Object findElement(int x, int y) {
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178 Enumeration keys = nameHash.keys();
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180 while (keys.hasMoreElements()) {
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181 Object ob = keys.nextElement();
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182 Rectangle rect = (Rectangle)nameHash.get(ob);
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184 if (x >= rect.x && x <= (rect.x + rect.width) &&
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185 y >= rect.y && y <= (rect.y + rect.height)) {
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189 keys = nodeHash.keys();
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191 while (keys.hasMoreElements()) {
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192 Object ob = keys.nextElement();
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193 Rectangle rect = (Rectangle)nodeHash.get(ob);
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195 if (x >= rect.x && x <= (rect.x + rect.width) &&
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196 y >= rect.y && y <= (rect.y + rect.height)) {
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204 public void pickNodes(Rectangle pickBox, Selection sel) {
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205 int width = getWidth();
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206 int height = getHeight();
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208 SequenceNode top = tree.getTopNode();
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210 float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()
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212 if (top.count == 0) {
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213 top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
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215 float chunk = (float)(height-offy*2)/top.count;
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217 pickNode(pickBox,sel,top,chunk,wscale,width,offx,offy);
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220 public void pickNode(Rectangle pickBox, Selection sel, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {
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221 if (node == null) {
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225 if (node.left() == null && node.right() == null) {
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226 float height = node.height;
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227 float dist = node.dist;
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229 int xstart = (int)((height-dist)*scale) + offx;
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230 int xend = (int)(height*scale) + offx;
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232 int ypos = (int)(node.ycount * chunk) + offy;
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234 if (pickBox.contains(new Point(xend,ypos))) {
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235 if (node.element() instanceof SequenceI) {
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236 SequenceI seq = (SequenceI)node.element();
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237 if (sel.contains(seq)) {
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238 sel.removeElement(seq);
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240 sel.addElement(seq);
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245 pickNode(pickBox,sel,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
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246 pickNode(pickBox,sel,(SequenceNode)node.right(),chunk,scale,width,offx,offy);
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250 public void setColor(SequenceNode node, Color c) {
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251 if (node == null) {
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255 if (node.left() == null && node.right() == null) {
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258 if (node.element() instanceof SequenceI) {
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259 ((SequenceI)node.element()).setColor(c);
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263 setColor((SequenceNode)node.left(),c);
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264 setColor((SequenceNode)node.right(),c);
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269 public void paintComponent(Graphics g) {
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272 font = new Font("Verdana",Font.PLAIN,fontSize);
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275 FontMetrics fm = g.getFontMetrics(font);
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277 if(nameHash.size()==0)
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281 if( scrollPane.getHeight() > fm.getHeight() * nameHash.size()+offy)
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283 draw(g,scrollPane.getWidth(),scrollPane.getHeight());
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284 setPreferredSize(new Dimension(scrollPane.getWidth(), scrollPane.getHeight()));
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288 setPreferredSize(new Dimension(getWidth(), fm.getHeight() * nameHash.size()));
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289 draw( g,getWidth(), fm.getHeight() * nameHash.size());
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293 if (threshold != 0)
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295 g.setColor(Color.red);
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296 g.drawLine(threshold,0,threshold,getHeight());
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299 scrollPane.revalidate();
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301 public int getFontSize() {
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304 public void setFontSize(int fontSize) {
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305 this.fontSize = fontSize;
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308 public void draw(Graphics g, int width, int height) {
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309 g.setColor(Color.white);
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310 g.fillRect(0,0,width,height);
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313 labelLength = g.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar
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315 float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();
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317 SequenceNode top = tree.getTopNode();
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319 if (top.count == 0) {
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320 top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
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322 float chunk = (float)(height-offy*2)/top.count ;
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324 drawNode(g,tree.getTopNode(),chunk,wscale,width,offx,offy);
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327 public void mouseReleased(MouseEvent e) { }
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328 public void mouseEntered(MouseEvent e) { }
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329 public void mouseExited(MouseEvent e) { }
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330 public void mouseClicked(MouseEvent e) {
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333 public void mousePressed(MouseEvent e) {
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337 Object ob = findElement(x,y);
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339 if (ob instanceof SequenceI)
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341 TreeSelectionChanged((Sequence)ob);
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345 } else if (ob instanceof SequenceNode) {
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346 SequenceNode tmpnode = (SequenceNode)ob;
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347 tree.swapNodes(tmpnode);
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348 tree.reCount(tree.getTopNode());
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349 tree.findHeight(tree.getTopNode());
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353 if (tree.getMaxHeight() != 0) {
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354 float fthreshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);
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355 this.threshold = x;
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356 tree.getGroups().removeAllElements();
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357 tree.groupNodes(tree.getTopNode(),fthreshold);
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358 setColor(tree.getTopNode(),Color.black);
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360 for (int i=0; i < tree.getGroups().size(); i++) {
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362 Color col = new Color((int)(Math.random()*255),
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363 (int)(Math.random()*255),
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364 (int)(Math.random()*255));
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365 setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());
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367 // l is vector of Objects
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368 // Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
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374 PaintRefresher.Refresh(this);
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379 public void setShowDistances(boolean state) {
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380 this.showDistances = state;
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384 public void setShowBootstrap(boolean state) {
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385 this.showBootstrap = state;
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