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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23 import javax.imageio.*;
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26 import java.awt.event.*;
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27 import java.awt.image.*;
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28 import javax.swing.*;
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30 import org.jibble.epsgraphics.*;
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31 import jalview.analysis.*;
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32 import jalview.datamodel.*;
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33 import jalview.io.*;
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34 import jalview.jbgui.*;
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36 public class TreePanel
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44 TreeCanvas treeCanvas;
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47 public TreePanel(AlignViewport av, Vector seqVector, String type,
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48 String pwtype, int s, int e)
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53 this.pwtype = pwtype;
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58 String longestName = "";
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59 seq = new Sequence[seqVector.size()];
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61 for (int i = 0; i < seqVector.size(); i++)
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63 seq[i] = (Sequence) seqVector.elementAt(i);
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65 if (seq[i].getName().length() > longestName.length())
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67 longestName = seq[i].getName();
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71 tree = new NJTree(seq, type, pwtype, start, end);
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73 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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74 treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
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75 setViewStateFromTreeCanvas(treeCanvas);
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76 tree.reCount(tree.getTopNode());
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77 tree.findHeight(tree.getTopNode());
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78 scrollPane.setViewportView(treeCanvas);
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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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86 // These are probably only arbitrary strings reflecting source of tree
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88 this.pwtype = pwtype;
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91 end = seqVector.size();
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93 String longestName = "";
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94 seq = new Sequence[seqVector.size()];
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96 for (int i = 0; i < seqVector.size(); i++)
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98 seq[i] = (Sequence) seqVector.elementAt(i);
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101 // This constructor matches sequence names to treenodes and sets up the tree layouts.
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102 tree = new NJTree(seq, newtree);
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104 // Now have to calculate longest name based on the leaves
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105 Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
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106 boolean has_placeholders = false;
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108 for (int i = 0; i < leaves.size(); i++)
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110 SequenceNode lf = (SequenceNode) leaves.elementAt(i);
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112 if (lf.isPlaceholder())
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114 has_placeholders = true;
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117 if (longestName.length() < ( (Sequence) lf.element()).getName()
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120 longestName = TreeCanvas.PLACEHOLDER +
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121 ( (Sequence) lf.element()).getName();
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125 tree.reCount(tree.getTopNode());
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126 tree.findHeight(tree.getTopNode());
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128 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
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129 treeCanvas.setShowBootstrap(newtree.HasBootstrap());
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130 treeCanvas.setShowDistances(newtree.HasDistances());
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131 scrollPane.setViewportView(treeCanvas);
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132 treeCanvas.setMarkPlaceholders(has_placeholders);
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133 setViewStateFromTreeCanvas(treeCanvas);
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135 // JBPNote TODO: preference for always marking placeholders in new associated tree
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138 public NJTree getTree()
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143 private void setViewStateFromTreeCanvas(TreeCanvas tree)
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145 // update view menu state from treeCanvas render state
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146 distanceMenu.setSelected(tree.showDistances);
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147 bootstrapMenu.setSelected(tree.showBootstrap);
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148 placeholdersMenu.setSelected(tree.markPlaceholders);
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151 private void setTreeCanvasFromViewState(TreeCanvas tree)
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153 // update view menu state from treeCanvas render state
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154 tree.showDistances = distanceMenu.isSelected();
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155 tree.showBootstrap = bootstrapMenu.isSelected();
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156 tree.markPlaceholders = placeholdersMenu.isSelected();
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159 public void textbox_actionPerformed(ActionEvent e)
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161 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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163 StringBuffer buffer = new StringBuffer();
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165 if (type.equals("AV"))
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167 buffer.append("Average distance tree using ");
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171 buffer.append("Neighbour joining tree using ");
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174 if (pwtype.equals("BL"))
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176 buffer.append("BLOSUM62");
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180 buffer.append("PID");
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183 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
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185 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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186 cap.setText(fout.print(false, true));
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189 public void saveAsNewick_actionPerformed(ActionEvent e)
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191 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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193 "LAST_DIRECTORY"));
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194 chooser.setFileView(new JalviewFileView());
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195 chooser.setDialogTitle("Save tree as newick file");
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196 chooser.setToolTipText("Save");
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198 int value = chooser.showSaveDialog(null);
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200 if (value == JalviewFileChooser.APPROVE_OPTION)
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202 String choice = chooser.getSelectedFile().getPath();
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203 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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204 chooser.getSelectedFile().getParent());
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208 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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209 String output = fout.print(false, true); // distances only
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210 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
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213 out.println(output);
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216 catch (Exception ex)
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218 ex.printStackTrace();
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223 public void printMenu_actionPerformed(ActionEvent e)
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225 //Putting in a thread avoids Swing painting problems
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226 treeCanvas.startPrinting();
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229 public void fitToWindow_actionPerformed(ActionEvent e)
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231 treeCanvas.fitToWindow = fitToWindow.isSelected();
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235 public void fontSize_actionPerformed(ActionEvent e)
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237 if (treeCanvas == null)
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242 String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
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245 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
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246 "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,
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250 "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"
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251 }, "Font Size - " + size);
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253 if (selection != null)
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255 fontSize.setText("Font Size - " + selection);
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257 int i = Integer.parseInt(selection.toString());
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258 treeCanvas.setFontSize(i);
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261 scrollPane.setViewportView(treeCanvas);
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264 public void distanceMenu_actionPerformed(ActionEvent e)
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266 treeCanvas.setShowDistances(distanceMenu.isSelected());
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269 public void bootstrapMenu_actionPerformed(ActionEvent e)
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271 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
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274 public void placeholdersMenu_actionPerformed(ActionEvent e)
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276 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
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279 public void epsTree_actionPerformed(ActionEvent e)
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281 int width = treeCanvas.getWidth();
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282 int height = treeCanvas.getHeight();
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286 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
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287 jalview.bin.Cache.getProperty(
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288 "LAST_DIRECTORY"), new String[]
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291 {"Encapsulated Postscript"},
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292 "Encapsulated Postscript");
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293 chooser.setFileView(new jalview.io.JalviewFileView());
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294 chooser.setDialogTitle("Create EPS file from tree");
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295 chooser.setToolTipText("Save");
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297 int value = chooser.showSaveDialog(this);
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299 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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304 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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305 chooser.getSelectedFile().getParent());
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307 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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308 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
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311 treeCanvas.draw(pg, width, height);
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316 catch (Exception ex)
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318 ex.printStackTrace();
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322 public void pngTree_actionPerformed(ActionEvent e)
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324 int width = treeCanvas.getWidth();
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325 int height = treeCanvas.getHeight();
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329 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
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330 jalview.bin.Cache.getProperty(
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331 "LAST_DIRECTORY"), new String[]
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334 {"Portable network graphics"},
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335 "Portable network graphics");
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337 chooser.setFileView(new jalview.io.JalviewFileView());
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338 chooser.setDialogTitle("Create PNG image from tree");
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339 chooser.setToolTipText("Save");
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341 int value = chooser.showSaveDialog(this);
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343 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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348 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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349 chooser.getSelectedFile().getParent());
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351 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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353 BufferedImage bi = new BufferedImage(width, height,
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354 BufferedImage.TYPE_INT_RGB);
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355 Graphics png = bi.getGraphics();
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357 treeCanvas.draw(png, width, height);
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359 ImageIO.write(bi, "png", out);
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362 catch (Exception ex)
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364 ex.printStackTrace();
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