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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21 import javax.swing.*;
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22 import java.awt.event.*;
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23 import jalview.datamodel.*;
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24 import jalview.schemes.*;
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25 import jalview.gui.*;
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26 import jalview.io.EBIFetchClient;
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27 import java.awt.event.ActionListener;
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28 import java.awt.event.ActionEvent;
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30 public class PDBViewer extends JInternalFrame implements Runnable
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34 PDBCanvas pdbcanvas;
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37 public PDBViewer(PDBEntry entry,
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39 SeqCanvas seqcanvas)
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45 catch (Exception ex)
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47 ex.printStackTrace();
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55 pdbcanvas = new PDBCanvas(seqcanvas, sequence);
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57 if(pdb.getFile()!=null)
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60 PDBfile pdbfile = new PDBfile(pdb.getFile(),
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61 jalview.io.AppletFormatAdapter.FILE);
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62 pdbcanvas.setPDBFile(pdbfile);
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64 }catch(java.io.IOException ex)
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66 ex.printStackTrace();
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71 Thread worker = new Thread(this);
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77 setContentPane(pdbcanvas);
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78 StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
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79 if(pdb.getProperty()!=null)
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81 if (pdb.getProperty().get("method")!=null)
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83 title.append(" Method: ");
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84 title.append(pdb.getProperty().get("method"));
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86 if (pdb.getProperty().get("chains") != null)
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88 title.append(" Chain:");
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89 title.append(pdb.getProperty().get("chains"));
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92 Desktop.addInternalFrame(this,title.toString(),400, 400);
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99 EBIFetchClient ebi = new EBIFetchClient();
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100 String query = "pdb:" + pdb.getId();
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101 String file = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
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104 PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
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105 pdbcanvas.setPDBFile(pdbfile);
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109 throw new Exception("Empty result for WSDbFetch Query: " + query);
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112 catch (Exception ex)
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114 ex.printStackTrace();
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115 showErrorMessage("Failed to retrieve PDB structure.");
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120 private void jbInit()
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123 this.addKeyListener(new KeyAdapter()
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125 public void keyPressed(KeyEvent evt)
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127 pdbcanvas.keyPressed(evt);
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131 this.setJMenuBar(jMenuBar1);
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132 fileMenu.setText("File");
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133 coloursMenu.setText("Colours");
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134 saveMenu.setActionCommand("Save Image");
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135 saveMenu.setText("Save As");
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136 png.setText("PNG");
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137 png.addActionListener(new ActionListener()
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139 public void actionPerformed(ActionEvent e)
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141 png_actionPerformed(e);
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144 eps.setText("EPS");
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145 eps.addActionListener(new ActionListener()
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147 public void actionPerformed(ActionEvent e)
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149 eps_actionPerformed(e);
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152 mapping.setText("View Mapping");
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153 mapping.addActionListener(new ActionListener()
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155 public void actionPerformed(ActionEvent e)
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157 mapping_actionPerformed(e);
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160 wire.setText("Wireframe");
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161 wire.addActionListener(new ActionListener()
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163 public void actionPerformed(ActionEvent e)
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165 wire_actionPerformed(e);
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168 depth.setSelected(true);
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169 depth.setText("Depthcue");
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170 depth.addActionListener(new ActionListener()
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172 public void actionPerformed(ActionEvent e)
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174 depth_actionPerformed(e);
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177 zbuffer.setSelected(true);
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178 zbuffer.setText("Z Buffering");
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179 zbuffer.addActionListener(new ActionListener()
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181 public void actionPerformed(ActionEvent e)
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183 zbuffer_actionPerformed(e);
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186 charge.setText("Charge & Cysteine");
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187 charge.addActionListener(new ActionListener()
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189 public void actionPerformed(ActionEvent e)
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191 charge_actionPerformed(e);
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194 chain.setText("By Chain");
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195 chain.addActionListener(new ActionListener()
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197 public void actionPerformed(ActionEvent e)
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199 chain_actionPerformed(e);
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202 seqButton.setSelected(true);
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203 seqButton.setText("By Sequence");
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204 seqButton.addActionListener(new ActionListener()
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206 public void actionPerformed(ActionEvent e)
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208 seqButton_actionPerformed(e);
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211 allchains.setSelected(true);
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212 allchains.setText("Show All Chains");
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213 allchains.addItemListener(new ItemListener()
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215 public void itemStateChanged(ItemEvent e)
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217 allchains_itemStateChanged(e);
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220 zappo.setText("Zappo");
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221 zappo.addActionListener(new ActionListener()
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223 public void actionPerformed(ActionEvent e)
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225 zappo_actionPerformed(e);
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228 taylor.setText("Taylor");
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229 taylor.addActionListener(new ActionListener()
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231 public void actionPerformed(ActionEvent e)
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233 taylor_actionPerformed(e);
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236 hydro.setText("Hydro");
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237 hydro.addActionListener(new ActionListener()
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239 public void actionPerformed(ActionEvent e)
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241 hydro_actionPerformed(e);
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244 helix.setText("Helix");
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245 helix.addActionListener(new ActionListener()
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247 public void actionPerformed(ActionEvent e)
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249 helix_actionPerformed(e);
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252 strand.setText("Strand");
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253 strand.addActionListener(new ActionListener()
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255 public void actionPerformed(ActionEvent e)
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257 strand_actionPerformed(e);
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260 turn.setText("Turn");
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261 turn.addActionListener(new ActionListener()
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263 public void actionPerformed(ActionEvent e)
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265 turn_actionPerformed(e);
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268 buried.setText("Buried");
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269 buried.addActionListener(new ActionListener()
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271 public void actionPerformed(ActionEvent e)
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273 buried_actionPerformed(e);
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276 user.setText("User Defined...");
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277 user.addActionListener(new ActionListener()
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279 public void actionPerformed(ActionEvent e)
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281 user_actionPerformed(e);
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284 viewMenu.setText("View");
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285 background.setText("Background Colour...");
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286 background.addActionListener(new ActionListener()
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288 public void actionPerformed(ActionEvent e)
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290 background_actionPerformed(e);
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293 jMenuBar1.add(fileMenu);
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294 jMenuBar1.add(coloursMenu);
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295 jMenuBar1.add(viewMenu);
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296 fileMenu.add(saveMenu);
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297 fileMenu.add(mapping);
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300 coloursMenu.add(seqButton);
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301 coloursMenu.add(chain);
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302 coloursMenu.add(charge);
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303 coloursMenu.add(zappo);
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304 coloursMenu.add(taylor);
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305 coloursMenu.add(hydro);
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306 coloursMenu.add(helix);
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307 coloursMenu.add(strand);
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308 coloursMenu.add(turn);
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309 coloursMenu.add(buried);
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310 coloursMenu.add(user);
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311 coloursMenu.add(background);
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312 ButtonGroup bg = new ButtonGroup();
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326 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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328 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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329 getUserColourSchemes().keys();
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331 while (userColours.hasMoreElements())
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333 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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334 nextElement().toString());
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335 radioItem.setName("USER_DEFINED");
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336 radioItem.addMouseListener(new MouseAdapter()
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338 public void mousePressed(MouseEvent evt)
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340 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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342 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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344 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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345 "Remove from default list?",
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346 "Remove user defined colour",
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347 JOptionPane.YES_NO_OPTION);
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348 if(option == JOptionPane.YES_OPTION)
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350 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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351 coloursMenu.remove(radioItem);
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354 radioItem.addActionListener(new ActionListener()
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356 public void actionPerformed(ActionEvent evt)
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358 user_actionPerformed(evt);
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364 radioItem.addActionListener(new ActionListener()
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366 public void actionPerformed(ActionEvent evt)
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368 user_actionPerformed(evt);
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371 coloursMenu.add(radioItem);
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376 viewMenu.add(wire);
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377 viewMenu.add(depth);
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378 viewMenu.add(zbuffer);
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379 viewMenu.add(allchains);
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382 JMenuBar jMenuBar1 = new JMenuBar();
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383 JMenu fileMenu = new JMenu();
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384 JMenu coloursMenu = new JMenu();
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385 JMenu saveMenu = new JMenu();
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386 JMenuItem png = new JMenuItem();
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387 JMenuItem eps = new JMenuItem();
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388 JMenuItem mapping = new JMenuItem();
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389 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
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390 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
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391 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
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392 JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
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394 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
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395 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
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396 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
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397 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
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398 JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
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399 JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
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400 JRadioButtonMenuItem user = new JRadioButtonMenuItem();
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401 JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
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402 JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
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403 JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
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404 JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
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405 JMenu viewMenu = new JMenu();
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406 JMenuItem background = new JMenuItem();
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411 * @param e DOCUMENT ME!
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413 public void eps_actionPerformed(ActionEvent e)
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415 makePDBImage(jalview.util.ImageMaker.EPS);
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421 * @param e DOCUMENT ME!
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423 public void png_actionPerformed(ActionEvent e)
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425 makePDBImage(jalview.util.ImageMaker.PNG);
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428 void makePDBImage(int type)
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430 int width = pdbcanvas.getWidth();
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431 int height = pdbcanvas.getHeight();
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433 jalview.util.ImageMaker im;
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435 if (type == jalview.util.ImageMaker.PNG)
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436 im = new jalview.util.ImageMaker(this,
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437 jalview.util.ImageMaker.PNG,
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438 "Make PNG image from view",
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442 im = new jalview.util.ImageMaker(this,
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443 jalview.util.ImageMaker.EPS,
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444 "Make EPS file from view",
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446 null, this.getTitle());
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448 if (im.getGraphics() != null)
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450 pdbcanvas.drawAll(im.getGraphics(), width, height);
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454 public void charge_actionPerformed(ActionEvent e)
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456 pdbcanvas.bysequence = false;
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457 pdbcanvas.pdb.setChargeColours();
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458 pdbcanvas.redrawneeded=true;
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459 pdbcanvas.repaint();
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462 public void hydro_actionPerformed(ActionEvent e)
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464 pdbcanvas.bysequence = false;
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465 pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
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466 pdbcanvas.redrawneeded=true;
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467 pdbcanvas.repaint();
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470 public void chain_actionPerformed(ActionEvent e)
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472 pdbcanvas.bysequence = false;
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473 pdbcanvas.pdb.setChainColours();
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474 pdbcanvas.redrawneeded=true;
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475 pdbcanvas.repaint();
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478 public void zbuffer_actionPerformed(ActionEvent e)
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480 pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
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481 pdbcanvas.redrawneeded=true;
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482 pdbcanvas.repaint();
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485 public void molecule_actionPerformed(ActionEvent e)
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487 pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
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488 pdbcanvas.redrawneeded=true;
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489 pdbcanvas.repaint();
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492 public void depth_actionPerformed(ActionEvent e)
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494 pdbcanvas.depthcue = ! pdbcanvas.depthcue;
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495 pdbcanvas.redrawneeded=true;
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496 pdbcanvas.repaint();
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499 public void wire_actionPerformed(ActionEvent e)
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501 pdbcanvas.wire = ! pdbcanvas.wire;
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502 pdbcanvas.redrawneeded=true;
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503 pdbcanvas.repaint();
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506 public void seqButton_actionPerformed(ActionEvent e)
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508 pdbcanvas.bysequence = true;
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509 pdbcanvas.updateSeqColours();
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513 public void mapping_actionPerformed(ActionEvent e)
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515 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
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516 Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
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517 cap.setText(pdbcanvas.mappingDetails.toString());
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520 public void allchains_itemStateChanged(ItemEvent e)
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522 pdbcanvas.setAllchainsVisible(allchains.getState());
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524 void showErrorMessage(String error)
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526 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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527 error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
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531 public void zappo_actionPerformed(ActionEvent e)
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533 pdbcanvas.bysequence = false;
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534 pdbcanvas.pdb.setColours(new ZappoColourScheme());
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535 pdbcanvas.redrawneeded=true;
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536 pdbcanvas.repaint();
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539 public void taylor_actionPerformed(ActionEvent e)
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541 pdbcanvas.bysequence = false;
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542 pdbcanvas.pdb.setColours(new TaylorColourScheme());
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543 pdbcanvas.redrawneeded=true;
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544 pdbcanvas.repaint();
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547 public void helix_actionPerformed(ActionEvent e)
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549 pdbcanvas.bysequence = false;
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550 pdbcanvas.pdb.setColours(new HelixColourScheme());
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551 pdbcanvas.redrawneeded=true;
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552 pdbcanvas.repaint();
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555 public void strand_actionPerformed(ActionEvent e)
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557 pdbcanvas.bysequence = false;
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558 pdbcanvas.pdb.setColours(new StrandColourScheme());
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559 pdbcanvas.redrawneeded=true;
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560 pdbcanvas.repaint();
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563 public void turn_actionPerformed(ActionEvent e)
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565 pdbcanvas.bysequence = false;
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566 pdbcanvas.pdb.setColours(new TurnColourScheme());
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567 pdbcanvas.redrawneeded=true;
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568 pdbcanvas.repaint();
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571 public void buried_actionPerformed(ActionEvent e)
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573 pdbcanvas.bysequence = false;
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574 pdbcanvas.pdb.setColours(new BuriedColourScheme());
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575 pdbcanvas.redrawneeded=true;
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576 pdbcanvas.repaint();
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579 public void user_actionPerformed(ActionEvent e)
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581 if (e.getActionCommand().equals("User Defined..."))
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583 new UserDefinedColours(pdbcanvas, null);
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587 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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588 getUserColourSchemes().get(e.getActionCommand());
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590 pdbcanvas.pdb.setColours(udc);
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591 pdbcanvas.redrawneeded=true;
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592 pdbcanvas.repaint();
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596 public void background_actionPerformed(ActionEvent e)
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598 java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",
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599 pdbcanvas.backgroundColour);
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603 pdbcanvas.backgroundColour = col;
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604 pdbcanvas.redrawneeded = true;
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605 pdbcanvas.repaint();
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