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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38 TreeCanvas treeCanvas;
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41 public NJTree getTree()
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47 * Creates a new TreePanel object.
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49 * @param av DOCUMENT ME!
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50 * @param seqVector DOCUMENT ME!
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51 * @param type DOCUMENT ME!
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52 * @param pwtype DOCUMENT ME!
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53 * @param s DOCUMENT ME!
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54 * @param e DOCUMENT ME!
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56 public TreePanel(AlignViewport av, Vector seqVector, String type,
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57 String pwtype, int s, int e)
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62 this.setMenuBar(jMenuBar1);
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64 catch (Exception ex)
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66 ex.printStackTrace();
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69 initTreePanel(av, seqVector, type, pwtype, s, e, null);
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73 * Creates a new TreePanel object.
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75 * @param av DOCUMENT ME!
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76 * @param seqVector DOCUMENT ME!
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77 * @param newtree DOCUMENT ME!
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78 * @param type DOCUMENT ME!
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79 * @param pwtype DOCUMENT ME!
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81 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
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82 String type, String pwtype)
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87 this.setMenuBar(jMenuBar1);
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91 e.printStackTrace();
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94 initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
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98 void initTreePanel(AlignViewport av, Vector seqVector, String type,
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99 String pwtype, int s, int e, NewickFile newTree)
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103 this.pwtype = pwtype;
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108 seq = new Sequence[seqVector.size()];
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109 for(int i=0; i<seqVector.size(); i++)
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110 seq[i] = (SequenceI)seqVector.elementAt(i);
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113 treeCanvas = new TreeCanvas(av, scrollPane);
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114 scrollPane.add(treeCanvas);
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117 TreeLoader tl = new TreeLoader(newTree);
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122 class TreeLoader extends Thread
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124 NewickFile newtree;
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126 public TreeLoader(NewickFile newtree)
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128 this.newtree = newtree;
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134 tree = new NJTree(seq, newtree);
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136 tree = new NJTree(seq, type, pwtype, start, end);
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138 tree.reCount(tree.getTopNode());
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139 tree.findHeight(tree.getTopNode());
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140 treeCanvas.setTree(tree);
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143 distanceMenu.setState(newtree.HasDistances());
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144 bootstrapMenu.setState(newtree.HasBootstrap());
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145 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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146 treeCanvas.setShowDistances(newtree.HasDistances());
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150 treeCanvas.repaint();
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155 public String getText(String format)
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160 protected void fitToWindow_actionPerformed(ActionEvent e)
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162 treeCanvas.fitToWindow = fitToWindow.getState();
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163 treeCanvas.repaint();
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166 public void newickOutput_actionPerformed(ActionEvent actionEvent)
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168 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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169 String output = fout.print(false, true);
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170 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
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171 cap.setText(output);
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172 java.awt.Frame frame = new java.awt.Frame();
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174 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
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177 public java.awt.Font getTreeFont()
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179 return treeCanvas.font;
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182 public void setTreeFont(java.awt.Font font)
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184 treeCanvas.font = font;
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185 treeCanvas.repaint();
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188 protected void fontSize_actionPerformed(ActionEvent e)
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190 if( treeCanvas==null )
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193 new FontChooser(this);
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196 protected void distanceMenu_actionPerformed(ActionEvent e)
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198 treeCanvas.setShowDistances(distanceMenu.getState());
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201 protected void bootstrapMenu_actionPerformed(ActionEvent e)
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203 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
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206 protected void placeholdersMenu_actionPerformed(ActionEvent e)
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208 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
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211 BorderLayout borderLayout1 = new BorderLayout();
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212 protected ScrollPane scrollPane = new ScrollPane();
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213 MenuBar jMenuBar1 = new MenuBar();
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214 Menu jMenu2 = new Menu();
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215 protected MenuItem fontSize = new MenuItem();
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216 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
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217 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
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218 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
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219 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
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220 Menu fileMenu = new Menu();
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221 MenuItem newickOutput = new MenuItem();
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223 private void jbInit() throws Exception {
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224 setLayout(borderLayout1);
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225 this.setBackground(Color.white);
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226 this.setFont(new java.awt.Font("Verdana", 0, 12));
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227 jMenu2.setLabel("View");
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228 fontSize.setLabel("Font...");
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229 fontSize.addActionListener(new java.awt.event.ActionListener() {
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230 public void actionPerformed(ActionEvent e) {
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231 fontSize_actionPerformed(e);
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234 bootstrapMenu.setLabel("Show Bootstrap Values");
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235 bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {
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236 public void itemStateChanged(ItemEvent e) {
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237 bootstrapMenu_actionPerformed(null);
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240 distanceMenu.setLabel("Show Distances");
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241 distanceMenu.addItemListener(new java.awt.event.ItemListener() {
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242 public void itemStateChanged(ItemEvent e) {
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243 distanceMenu_actionPerformed(null);
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246 placeholdersMenu.setLabel("Mark Unassociated Leaves");
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247 placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {
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248 public void itemStateChanged(ItemEvent e) {
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249 placeholdersMenu_actionPerformed(null);
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252 fitToWindow.setState(true);
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253 fitToWindow.setLabel("Fit To Window");
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254 fitToWindow.addItemListener(new java.awt.event.ItemListener() {
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255 public void itemStateChanged(ItemEvent e) {
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256 fitToWindow_actionPerformed(null);
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259 fileMenu.setLabel("File");
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260 newickOutput.setLabel("Newick Format");
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261 newickOutput.addActionListener(new ActionListener() {
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262 public void actionPerformed(ActionEvent actionEvent) {
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263 newickOutput_actionPerformed(actionEvent);
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267 add(scrollPane, BorderLayout.CENTER);
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268 jMenuBar1.add(fileMenu);
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269 jMenuBar1.add(jMenu2);
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270 jMenu2.add(fitToWindow);
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271 jMenu2.add(fontSize);
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272 jMenu2.add(distanceMenu);
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273 jMenu2.add(bootstrapMenu);
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274 jMenu2.add(placeholdersMenu);
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275 fileMenu.add(newickOutput);
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