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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20 package jalview.appletgui;
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24 import java.awt.event.*;
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27 import jalview.analysis.*;
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28 import jalview.datamodel.*;
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29 import jalview.io.*;
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31 public class TreePanel extends Frame
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39 TreeCanvas treeCanvas;
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42 public NJTree getTree()
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48 * Creates a new TreePanel object.
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50 * @param av DOCUMENT ME!
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51 * @param seqVector DOCUMENT ME!
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52 * @param type DOCUMENT ME!
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53 * @param pwtype DOCUMENT ME!
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54 * @param s DOCUMENT ME!
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55 * @param e DOCUMENT ME!
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57 public TreePanel(AlignViewport av, Vector seqVector, String type,
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58 String pwtype, int s, int e)
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63 this.setMenuBar(jMenuBar1);
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65 catch (Exception ex)
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67 ex.printStackTrace();
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70 initTreePanel(av, seqVector, type, pwtype, s, e, null);
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74 * Creates a new TreePanel object.
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76 * @param av DOCUMENT ME!
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77 * @param seqVector DOCUMENT ME!
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78 * @param newtree DOCUMENT ME!
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79 * @param type DOCUMENT ME!
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80 * @param pwtype DOCUMENT ME!
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82 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
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83 String type, String pwtype)
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88 this.setMenuBar(jMenuBar1);
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92 e.printStackTrace();
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95 initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
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99 void initTreePanel(AlignViewport av, Vector seqVector, String type,
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100 String pwtype, int s, int e, NewickFile newTree)
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104 this.pwtype = pwtype;
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109 seq = new Sequence[seqVector.size()];
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110 for(int i=0; i<seqVector.size(); i++)
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111 seq[i] = (SequenceI)seqVector.elementAt(i);
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114 treeCanvas = new TreeCanvas(av, scrollPane);
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115 scrollPane.add(treeCanvas);
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118 TreeLoader tl = new TreeLoader(newTree);
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123 class TreeLoader extends Thread
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125 NewickFile newtree;
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127 public TreeLoader(NewickFile newtree)
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129 this.newtree = newtree;
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135 tree = new NJTree(seq, newtree);
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137 tree = new NJTree(seq, type, pwtype, start, end);
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139 tree.reCount(tree.getTopNode());
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140 tree.findHeight(tree.getTopNode());
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141 treeCanvas.setTree(tree);
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144 distanceMenu.setState(newtree.HasDistances());
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145 bootstrapMenu.setState(newtree.HasBootstrap());
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146 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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147 treeCanvas.setShowDistances(newtree.HasDistances());
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151 treeCanvas.repaint();
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156 public String getText(String format)
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161 protected void fitToWindow_actionPerformed(ActionEvent e)
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163 treeCanvas.fitToWindow = fitToWindow.getState();
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164 treeCanvas.repaint();
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167 public void newickOutput_actionPerformed(ActionEvent actionEvent)
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169 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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170 String output = fout.print(false, true);
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171 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
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172 cap.setText(output);
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173 java.awt.Frame frame = new java.awt.Frame();
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175 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
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178 public java.awt.Font getTreeFont()
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180 return treeCanvas.font;
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183 public void setTreeFont(java.awt.Font font)
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185 treeCanvas.font = font;
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186 treeCanvas.repaint();
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189 protected void fontSize_actionPerformed(ActionEvent e)
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191 if( treeCanvas==null )
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194 new FontChooser(this);
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197 protected void distanceMenu_actionPerformed(ActionEvent e)
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199 treeCanvas.setShowDistances(distanceMenu.getState());
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202 protected void bootstrapMenu_actionPerformed(ActionEvent e)
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204 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
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207 protected void placeholdersMenu_actionPerformed(ActionEvent e)
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209 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
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212 BorderLayout borderLayout1 = new BorderLayout();
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213 protected ScrollPane scrollPane = new ScrollPane();
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214 MenuBar jMenuBar1 = new MenuBar();
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215 Menu jMenu2 = new Menu();
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216 protected MenuItem fontSize = new MenuItem();
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217 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
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218 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
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219 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
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220 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
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221 Menu fileMenu = new Menu();
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222 MenuItem newickOutput = new MenuItem();
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223 CheckboxMenuItem fullId = new CheckboxMenuItem();
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225 private void jbInit() throws Exception {
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226 setLayout(borderLayout1);
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227 this.setBackground(Color.white);
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228 this.setFont(new java.awt.Font("Verdana", 0, 12));
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229 jMenu2.setLabel("View");
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230 fontSize.setLabel("Font...");
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231 fontSize.addActionListener(new java.awt.event.ActionListener() {
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232 public void actionPerformed(ActionEvent e) {
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233 fontSize_actionPerformed(e);
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236 bootstrapMenu.setLabel("Show Bootstrap Values");
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237 bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {
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238 public void itemStateChanged(ItemEvent e) {
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239 bootstrapMenu_actionPerformed(null);
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242 distanceMenu.setLabel("Show Distances");
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243 distanceMenu.addItemListener(new java.awt.event.ItemListener() {
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244 public void itemStateChanged(ItemEvent e) {
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245 distanceMenu_actionPerformed(null);
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248 placeholdersMenu.setLabel("Mark Unassociated Leaves");
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249 placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {
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250 public void itemStateChanged(ItemEvent e) {
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251 placeholdersMenu_actionPerformed(null);
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254 fitToWindow.setState(true);
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255 fitToWindow.setLabel("Fit To Window");
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256 fitToWindow.addItemListener(new java.awt.event.ItemListener() {
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257 public void itemStateChanged(ItemEvent e) {
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258 fitToWindow_actionPerformed(null);
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261 fileMenu.setLabel("File");
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262 newickOutput.setLabel("Newick Format");
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263 newickOutput.addActionListener(new ActionListener() {
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264 public void actionPerformed(ActionEvent actionEvent) {
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265 newickOutput_actionPerformed(actionEvent);
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268 fullId.setLabel("Show Full Id");
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269 fullId.addItemListener(new ItemListener()
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271 public void itemStateChanged(ItemEvent itemEvent)
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273 fullId_itemStateChanged(itemEvent);
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277 add(scrollPane, BorderLayout.CENTER);
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278 jMenuBar1.add(fileMenu);
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279 jMenuBar1.add(jMenu2);
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280 jMenu2.add(fitToWindow);
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281 jMenu2.add(fontSize);
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282 jMenu2.add(distanceMenu);
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283 jMenu2.add(bootstrapMenu);
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284 jMenu2.add(placeholdersMenu);
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285 jMenu2.add(fullId);
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286 fullId.setState(true);
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287 fileMenu.add(newickOutput);
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291 public void fullId_itemStateChanged(ItemEvent itemEvent)
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293 tree.findHeight(tree.getTopNode());
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295 // Now have to calculate longest name based on the leaves
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296 Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
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298 treeCanvas.longestName="";
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299 for (int i = 0; i < leaves.size(); i++)
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301 SequenceNode lf = (SequenceNode) leaves.elementAt(i);
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302 Sequence seq = (Sequence) lf.element();
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303 lf.setName(seq.getDisplayId(fullId.getState(), false));
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304 if(lf.getName().length() > treeCanvas.longestName.length())
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305 treeCanvas.longestName = lf.getName();
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308 treeCanvas.repaint();
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