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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21 import jalview.analysis.*;
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23 import jalview.datamodel.*;
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25 import jalview.io.*;
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27 import jalview.jbgui.*;
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29 import org.jibble.epsgraphics.*;
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32 import java.awt.event.*;
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33 import java.awt.image.*;
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39 import javax.imageio.*;
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41 import java.beans.PropertyChangeEvent;
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48 * @version $Revision$
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50 public class TreePanel extends GTreePanel
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57 TreeCanvas treeCanvas;
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62 * Creates a new TreePanel object.
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64 * @param av DOCUMENT ME!
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65 * @param seqVector DOCUMENT ME!
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66 * @param type DOCUMENT ME!
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67 * @param pwtype DOCUMENT ME!
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68 * @param s DOCUMENT ME!
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69 * @param e DOCUMENT ME!
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71 public TreePanel(AlignViewport av, Vector seqVector, String type,
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72 String pwtype, int s, int e)
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75 initTreePanel(av, seqVector, type, pwtype, s, e, null);
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77 // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
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78 showDistances(true);
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82 * Creates a new TreePanel object.
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84 * @param av DOCUMENT ME!
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85 * @param seqVector DOCUMENT ME!
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86 * @param newtree DOCUMENT ME!
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87 * @param type DOCUMENT ME!
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88 * @param pwtype DOCUMENT ME!
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90 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
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91 String type, String pwtype)
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94 initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
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97 public AlignmentI getAlignment()
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99 return treeCanvas.av.getAlignment();
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103 void initTreePanel(AlignViewport av, Vector seqVector, String type,
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104 String pwtype, int s, int e, NewickFile newTree)
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108 this.pwtype = pwtype;
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113 seq = new Sequence[seqVector.size()];
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114 seqVector.toArray(seq);
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117 treeCanvas = new TreeCanvas(av, scrollPane);
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118 scrollPane.setViewportView(treeCanvas);
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120 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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122 public void propertyChange(PropertyChangeEvent evt)
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124 if (evt.getPropertyName().equals("alignment"))
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127 System.out.println("tree is null");
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128 if(evt.getNewValue()==null)
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129 System.out.println("new value is null");
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131 tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
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141 TreeLoader tl = new TreeLoader(newTree);
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146 class TreeLoader extends Thread
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148 NewickFile newtree;
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150 public TreeLoader(NewickFile newtree)
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152 this.newtree = newtree;
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153 if (newtree != null)
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155 // Must be outside run(), as Jalview2XML tries to
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156 // update distance/bootstrap visibility at the same time
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157 showBootstrap(newtree.HasBootstrap());
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158 showDistances(newtree.HasDistances());
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165 tree = new NJTree(seq, newtree);
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167 tree = new NJTree(seq, type, pwtype, start, end);
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169 tree.reCount(tree.getTopNode());
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170 tree.findHeight(tree.getTopNode());
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171 treeCanvas.setTree(tree);
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173 treeCanvas.repaint();
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175 av.setCurrentTree(tree);
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180 public void showDistances(boolean b)
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182 treeCanvas.setShowDistances(b);
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183 distanceMenu.setSelected(b);
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186 public void showBootstrap(boolean b)
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188 treeCanvas.setShowBootstrap(b);
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189 bootstrapMenu.setSelected(b);
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192 public void showPlaceholders(boolean b)
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194 placeholdersMenu.setState(b);
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195 treeCanvas.setMarkPlaceholders(b);
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204 * @return DOCUMENT ME!
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206 public NJTree getTree()
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215 * @param e DOCUMENT ME!
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217 public void textbox_actionPerformed(ActionEvent e)
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219 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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221 StringBuffer buffer = new StringBuffer();
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223 if (type.equals("AV"))
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225 buffer.append("Average distance tree using ");
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229 buffer.append("Neighbour joining tree using ");
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232 if (pwtype.equals("BL"))
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234 buffer.append("BLOSUM62");
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238 buffer.append("PID");
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241 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
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243 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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244 cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
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250 * @param e DOCUMENT ME!
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252 public void saveAsNewick_actionPerformed(ActionEvent e)
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254 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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255 "LAST_DIRECTORY"));
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256 chooser.setFileView(new JalviewFileView());
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257 chooser.setDialogTitle("Save tree as newick file");
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258 chooser.setToolTipText("Save");
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260 int value = chooser.showSaveDialog(null);
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262 if (value == JalviewFileChooser.APPROVE_OPTION)
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264 String choice = chooser.getSelectedFile().getPath();
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265 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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266 chooser.getSelectedFile().getParent());
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270 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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271 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
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272 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
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274 out.println(output);
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277 catch (Exception ex)
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279 ex.printStackTrace();
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287 * @param e DOCUMENT ME!
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289 public void printMenu_actionPerformed(ActionEvent e)
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291 //Putting in a thread avoids Swing painting problems
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292 treeCanvas.startPrinting();
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298 * @param e DOCUMENT ME!
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300 public void fitToWindow_actionPerformed(ActionEvent e)
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302 treeCanvas.fitToWindow = fitToWindow.isSelected();
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309 * @param e DOCUMENT ME!
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311 public void font_actionPerformed(ActionEvent e)
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313 if (treeCanvas == null)
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318 new FontChooser(this);
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321 public Font getTreeFont()
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323 return treeCanvas.font;
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326 public void setTreeFont(Font font)
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328 if(treeCanvas!=null)
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329 treeCanvas.setFont(font);
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335 * @param e DOCUMENT ME!
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337 public void distanceMenu_actionPerformed(ActionEvent e)
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339 treeCanvas.setShowDistances(distanceMenu.isSelected());
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345 * @param e DOCUMENT ME!
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347 public void bootstrapMenu_actionPerformed(ActionEvent e)
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349 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
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355 * @param e DOCUMENT ME!
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357 public void placeholdersMenu_actionPerformed(ActionEvent e)
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359 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
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365 * @param e DOCUMENT ME!
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367 public void epsTree_actionPerformed(ActionEvent e)
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369 boolean accurateText = true;
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371 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
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372 "Prompt each time");
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374 // If we need to prompt, and if the GUI is visible then
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375 // Prompt for EPS rendering style
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376 if (renderStyle.equalsIgnoreCase("Prompt each time")
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378 (System.getProperty("java.awt.headless") != null
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379 && System.getProperty("java.awt.headless").equals("true")))
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381 EPSOptions eps = new EPSOptions();
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382 renderStyle = eps.getValue();
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384 if (renderStyle==null || eps.cancelled)
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390 if (renderStyle.equalsIgnoreCase("text"))
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392 accurateText = false;
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395 int width = treeCanvas.getWidth();
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396 int height = treeCanvas.getHeight();
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400 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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401 "LAST_DIRECTORY"), new String[] { "eps" },
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402 new String[] { "Encapsulated Postscript" },
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403 "Encapsulated Postscript");
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404 chooser.setFileView(new jalview.io.JalviewFileView());
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405 chooser.setDialogTitle("Create EPS file from tree");
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406 chooser.setToolTipText("Save");
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408 int value = chooser.showSaveDialog(this);
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410 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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415 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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416 chooser.getSelectedFile().getParent());
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418 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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419 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
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422 pg.setAccurateTextMode(accurateText);
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424 treeCanvas.draw(pg, width, height);
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429 catch (Exception ex)
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431 ex.printStackTrace();
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438 * @param e DOCUMENT ME!
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440 public void pngTree_actionPerformed(ActionEvent e)
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442 int width = treeCanvas.getWidth();
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443 int height = treeCanvas.getHeight();
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447 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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448 "LAST_DIRECTORY"), new String[] { "png" },
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449 new String[] { "Portable network graphics" },
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450 "Portable network graphics");
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452 chooser.setFileView(new jalview.io.JalviewFileView());
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453 chooser.setDialogTitle("Create PNG image from tree");
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454 chooser.setToolTipText("Save");
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456 int value = chooser.showSaveDialog(this);
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458 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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463 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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464 chooser.getSelectedFile().getParent());
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466 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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468 BufferedImage bi = new BufferedImage(width, height,
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469 BufferedImage.TYPE_INT_RGB);
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470 Graphics png = bi.getGraphics();
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472 treeCanvas.draw(png, width, height);
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474 ImageIO.write(bi, "png", out);
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477 catch (Exception ex)
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479 ex.printStackTrace();
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