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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61 * Creates a new TreePanel object.
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63 * @param av DOCUMENT ME!
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64 * @param seqVector DOCUMENT ME!
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65 * @param type DOCUMENT ME!
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66 * @param pwtype DOCUMENT ME!
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67 * @param s DOCUMENT ME!
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68 * @param e DOCUMENT ME!
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70 public TreePanel(AlignViewport av, Vector seqVector, String type,
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71 String pwtype, int s, int e)
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74 initTreePanel(av, seqVector, type, pwtype, s, e, null);
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76 // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
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77 showDistances(true);
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81 * Creates a new TreePanel object.
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83 * @param av DOCUMENT ME!
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84 * @param seqVector DOCUMENT ME!
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85 * @param newtree DOCUMENT ME!
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86 * @param type DOCUMENT ME!
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87 * @param pwtype DOCUMENT ME!
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89 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
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90 String type, String pwtype)
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93 initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
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96 public AlignmentI getAlignment()
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98 return treeCanvas.av.getAlignment();
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102 void initTreePanel(AlignViewport av, Vector seqVector, String type,
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103 String pwtype, int s, int e, NewickFile newTree)
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107 this.pwtype = pwtype;
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112 seq = new Sequence[seqVector.size()];
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113 seqVector.toArray(seq);
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116 treeCanvas = new TreeCanvas(av, scrollPane);
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117 scrollPane.setViewportView(treeCanvas);
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119 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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121 public void propertyChange(PropertyChangeEvent evt)
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123 if (evt.getPropertyName().equals("alignment"))
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126 System.out.println("tree is null");
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127 if(evt.getNewValue()==null)
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128 System.out.println("new value is null");
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130 tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
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138 TreeLoader tl = new TreeLoader(newTree);
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143 class TreeLoader extends Thread
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145 NewickFile newtree;
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147 public TreeLoader(NewickFile newtree)
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149 this.newtree = newtree;
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150 if (newtree != null)
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152 // Must be outside run(), as Jalview2XML tries to
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153 // update distance/bootstrap visibility at the same time
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154 showBootstrap(newtree.HasBootstrap());
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155 showDistances(newtree.HasDistances());
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156 showPlaceholders(true);
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163 tree = new NJTree(seq, newtree);
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165 tree = new NJTree(seq, type, pwtype, start, end);
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167 tree.reCount(tree.getTopNode());
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168 tree.findHeight(tree.getTopNode());
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169 treeCanvas.setTree(tree);
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171 treeCanvas.repaint();
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174 fullid.setState(treeCanvas.av.showDBPrefix);
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175 if(!treeCanvas.av.showDBPrefix)
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177 fullid_actionPerformed(null);
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183 public void showDistances(boolean b)
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185 treeCanvas.setShowDistances(b);
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186 distanceMenu.setSelected(b);
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189 public void showBootstrap(boolean b)
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191 treeCanvas.setShowBootstrap(b);
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192 bootstrapMenu.setSelected(b);
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195 public void showPlaceholders(boolean b)
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197 placeholdersMenu.setState(b);
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198 treeCanvas.setMarkPlaceholders(b);
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207 * @return DOCUMENT ME!
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209 public NJTree getTree()
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218 * @param e DOCUMENT ME!
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220 public void textbox_actionPerformed(ActionEvent e)
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222 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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224 StringBuffer buffer = new StringBuffer();
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226 if (type.equals("AV"))
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228 buffer.append("Average distance tree using ");
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232 buffer.append("Neighbour joining tree using ");
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235 if (pwtype.equals("BL"))
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237 buffer.append("BLOSUM62");
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241 buffer.append("PID");
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244 Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
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246 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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247 cap.setText(fout.print(false, true));
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253 * @param e DOCUMENT ME!
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255 public void saveAsNewick_actionPerformed(ActionEvent e)
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257 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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258 "LAST_DIRECTORY"));
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259 chooser.setFileView(new JalviewFileView());
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260 chooser.setDialogTitle("Save tree as newick file");
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261 chooser.setToolTipText("Save");
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263 int value = chooser.showSaveDialog(null);
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265 if (value == JalviewFileChooser.APPROVE_OPTION)
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267 String choice = chooser.getSelectedFile().getPath();
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268 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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269 chooser.getSelectedFile().getParent());
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273 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
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274 String output = fout.print(false, true); // distances only
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275 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
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277 out.println(output);
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280 catch (Exception ex)
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282 ex.printStackTrace();
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290 * @param e DOCUMENT ME!
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292 public void printMenu_actionPerformed(ActionEvent e)
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294 //Putting in a thread avoids Swing painting problems
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295 treeCanvas.startPrinting();
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301 * @param e DOCUMENT ME!
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303 public void fitToWindow_actionPerformed(ActionEvent e)
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305 treeCanvas.fitToWindow = fitToWindow.isSelected();
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312 * @param e DOCUMENT ME!
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314 public void font_actionPerformed(ActionEvent e)
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316 if (treeCanvas == null)
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321 new FontChooser(this);
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324 public Font getTreeFont()
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326 return treeCanvas.font;
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329 public void setTreeFont(Font font)
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331 if(treeCanvas!=null)
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332 treeCanvas.setFont(font);
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338 * @param e DOCUMENT ME!
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340 public void distanceMenu_actionPerformed(ActionEvent e)
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342 treeCanvas.setShowDistances(distanceMenu.isSelected());
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348 * @param e DOCUMENT ME!
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350 public void bootstrapMenu_actionPerformed(ActionEvent e)
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352 treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
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358 * @param e DOCUMENT ME!
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360 public void placeholdersMenu_actionPerformed(ActionEvent e)
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362 treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
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366 public void fullid_actionPerformed(ActionEvent e)
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368 tree.findHeight(tree.getTopNode());
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370 // Now have to calculate longest name based on the leaves
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371 Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
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373 treeCanvas.longestName="";
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374 for (int i = 0; i < leaves.size(); i++)
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376 SequenceNode lf = (SequenceNode) leaves.elementAt(i);
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377 Sequence seq = (Sequence) lf.element();
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378 lf.setName(seq.getDisplayId(fullid.getState(), false));
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379 if(lf.getName().length() > treeCanvas.longestName.length())
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380 treeCanvas.longestName = lf.getName();
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383 treeCanvas.repaint();
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390 * @param e DOCUMENT ME!
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392 public void epsTree_actionPerformed(ActionEvent e)
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394 boolean accurateText = true;
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396 String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
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397 "Prompt each time");
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399 // If we need to prompt, and if the GUI is visible then
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400 // Prompt for EPS rendering style
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401 if (renderStyle.equalsIgnoreCase("Prompt each time")
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403 (System.getProperty("java.awt.headless") != null
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404 && System.getProperty("java.awt.headless").equals("true")))
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406 EPSOptions eps = new EPSOptions();
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407 renderStyle = eps.getValue();
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409 if (renderStyle==null || eps.cancelled)
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415 if (renderStyle.equalsIgnoreCase("text"))
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417 accurateText = false;
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420 int width = treeCanvas.getWidth();
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421 int height = treeCanvas.getHeight();
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425 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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426 "LAST_DIRECTORY"), new String[] { "eps" },
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427 new String[] { "Encapsulated Postscript" },
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428 "Encapsulated Postscript");
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429 chooser.setFileView(new jalview.io.JalviewFileView());
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430 chooser.setDialogTitle("Create EPS file from tree");
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431 chooser.setToolTipText("Save");
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433 int value = chooser.showSaveDialog(this);
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435 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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440 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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441 chooser.getSelectedFile().getParent());
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443 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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444 EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
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447 pg.setAccurateTextMode(accurateText);
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449 treeCanvas.draw(pg, width, height);
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454 catch (Exception ex)
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456 ex.printStackTrace();
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463 * @param e DOCUMENT ME!
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465 public void pngTree_actionPerformed(ActionEvent e)
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467 int width = treeCanvas.getWidth();
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468 int height = treeCanvas.getHeight();
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472 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
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473 "LAST_DIRECTORY"), new String[] { "png" },
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474 new String[] { "Portable network graphics" },
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475 "Portable network graphics");
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477 chooser.setFileView(new jalview.io.JalviewFileView());
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478 chooser.setDialogTitle("Create PNG image from tree");
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479 chooser.setToolTipText("Save");
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481 int value = chooser.showSaveDialog(this);
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483 if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
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488 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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489 chooser.getSelectedFile().getParent());
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491 FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
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493 BufferedImage bi = new BufferedImage(width, height,
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494 BufferedImage.TYPE_INT_RGB);
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495 Graphics png = bi.getGraphics();
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497 treeCanvas.draw(png, width, height);
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499 ImageIO.write(bi, "png", out);
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502 catch (Exception ex)
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504 ex.printStackTrace();
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