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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41 /*Uncomment this to modify in Jbuilder
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46 catch (Exception ex)
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48 ex.printStackTrace();
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56 Thread worker = new Thread(this);
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59 pdbcanvas = new PDBCanvas(seqcanvas, seq);
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61 setContentPane(pdbcanvas);
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62 StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
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63 if(pdb.getProperty()!=null)
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65 if (pdb.getProperty().get("method")!=null)
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67 title.append(" Method: ");
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68 title.append(pdb.getProperty().get("method"));
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70 if (pdb.getProperty().get("chains") != null)
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72 title.append(" Chain:");
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73 title.append(pdb.getProperty().get("chains"));
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76 Desktop.addInternalFrame(this,title.toString(),400, 400);
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83 EBIFetchClient ebi = new EBIFetchClient();
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84 String query = "pdb:" + pdb.getId();
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85 String[] result = ebi.fetchData(query, "default","raw");
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87 PDBfile pdbfile = new PDBfile(result);
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88 pdbcanvas.setPDBFile(pdbfile);
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90 throw new Exception("Empty result for WSDbFetch Query: "+query);
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97 catch (Exception ex)
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99 ex.printStackTrace();
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102 catch (Exception ex)
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104 ex.printStackTrace();
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105 showErrorMessage("Failed to retrieve PDB structure.");
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110 private void jbInit()
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113 this.addKeyListener(new KeyAdapter()
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115 public void keyPressed(KeyEvent evt)
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117 pdbcanvas.keyPressed(evt);
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121 this.setJMenuBar(jMenuBar1);
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122 fileMenu.setText("File");
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123 coloursMenu.setText("Colours");
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124 saveMenu.setActionCommand("Save Image");
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125 saveMenu.setText("Save As");
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126 png.setText("PNG");
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127 png.addActionListener(new ActionListener()
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129 public void actionPerformed(ActionEvent e)
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131 png_actionPerformed(e);
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134 eps.setText("EPS");
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135 eps.addActionListener(new ActionListener()
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137 public void actionPerformed(ActionEvent e)
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139 eps_actionPerformed(e);
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142 mapping.setText("View Mapping");
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143 mapping.addActionListener(new ActionListener()
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145 public void actionPerformed(ActionEvent e)
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147 mapping_actionPerformed(e);
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150 wire.setText("Wireframe");
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151 wire.addActionListener(new ActionListener()
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153 public void actionPerformed(ActionEvent e)
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155 wire_actionPerformed(e);
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158 depth.setSelected(true);
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159 depth.setText("Depthcue");
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160 depth.addActionListener(new ActionListener()
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162 public void actionPerformed(ActionEvent e)
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164 depth_actionPerformed(e);
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167 zbuffer.setSelected(true);
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168 zbuffer.setText("Z Buffering");
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169 zbuffer.addActionListener(new ActionListener()
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171 public void actionPerformed(ActionEvent e)
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173 zbuffer_actionPerformed(e);
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176 charge.setText("Charge & Cysteine");
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177 charge.addActionListener(new ActionListener()
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179 public void actionPerformed(ActionEvent e)
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181 charge_actionPerformed(e);
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184 chain.setText("By Chain");
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185 chain.addActionListener(new ActionListener()
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187 public void actionPerformed(ActionEvent e)
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189 chain_actionPerformed(e);
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192 seqButton.setSelected(true);
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193 seqButton.setText("By Sequence");
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194 seqButton.addActionListener(new ActionListener()
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196 public void actionPerformed(ActionEvent e)
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198 seqButton_actionPerformed(e);
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201 allchains.setSelected(true);
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202 allchains.setText("Show All Chains");
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203 allchains.addItemListener(new ItemListener()
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205 public void itemStateChanged(ItemEvent e)
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207 allchains_itemStateChanged(e);
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210 zappo.setText("Zappo");
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211 zappo.addActionListener(new ActionListener()
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213 public void actionPerformed(ActionEvent e)
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215 zappo_actionPerformed(e);
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218 taylor.setText("Taylor");
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219 taylor.addActionListener(new ActionListener()
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221 public void actionPerformed(ActionEvent e)
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223 taylor_actionPerformed(e);
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226 hydro.setText("Hydro");
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227 hydro.addActionListener(new ActionListener()
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229 public void actionPerformed(ActionEvent e)
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231 hydro_actionPerformed(e);
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234 helix.setText("Helix");
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235 helix.addActionListener(new ActionListener()
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237 public void actionPerformed(ActionEvent e)
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239 helix_actionPerformed(e);
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242 strand.setText("Strand");
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243 strand.addActionListener(new ActionListener()
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245 public void actionPerformed(ActionEvent e)
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247 strand_actionPerformed(e);
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250 turn.setText("Turn");
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251 turn.addActionListener(new ActionListener()
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253 public void actionPerformed(ActionEvent e)
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255 turn_actionPerformed(e);
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258 buried.setText("Buried");
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259 buried.addActionListener(new ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 buried_actionPerformed(e);
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266 user.setText("User Defined...");
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267 user.addActionListener(new ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 user_actionPerformed(e);
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274 viewMenu.setText("View");
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275 background.setText("Background Colour...");
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276 background.addActionListener(new ActionListener()
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278 public void actionPerformed(ActionEvent e)
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280 background_actionPerformed(e);
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283 jMenuBar1.add(fileMenu);
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284 jMenuBar1.add(coloursMenu);
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285 jMenuBar1.add(viewMenu);
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286 fileMenu.add(saveMenu);
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287 fileMenu.add(mapping);
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290 coloursMenu.add(seqButton);
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291 coloursMenu.add(chain);
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292 coloursMenu.add(charge);
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293 coloursMenu.add(zappo);
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294 coloursMenu.add(taylor);
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295 coloursMenu.add(hydro);
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296 coloursMenu.add(helix);
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297 coloursMenu.add(strand);
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298 coloursMenu.add(turn);
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299 coloursMenu.add(buried);
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300 coloursMenu.add(user);
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301 coloursMenu.add(background);
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302 ButtonGroup bg = new ButtonGroup();
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316 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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318 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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319 getUserColourSchemes().keys();
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321 while (userColours.hasMoreElements())
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323 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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324 nextElement().toString());
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325 radioItem.setName("USER_DEFINED");
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326 radioItem.addMouseListener(new MouseAdapter()
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328 public void mousePressed(MouseEvent evt)
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330 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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332 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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334 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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335 "Remove from default list?",
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336 "Remove user defined colour",
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337 JOptionPane.YES_NO_OPTION);
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338 if(option == JOptionPane.YES_OPTION)
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340 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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341 coloursMenu.remove(radioItem);
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344 radioItem.addActionListener(new ActionListener()
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346 public void actionPerformed(ActionEvent evt)
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348 user_actionPerformed(evt);
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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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361 coloursMenu.add(radioItem);
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366 viewMenu.add(wire);
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367 viewMenu.add(depth);
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368 viewMenu.add(zbuffer);
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369 viewMenu.add(allchains);
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372 JMenuBar jMenuBar1 = new JMenuBar();
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373 JMenu fileMenu = new JMenu();
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374 JMenu coloursMenu = new JMenu();
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375 JMenu saveMenu = new JMenu();
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376 JMenuItem png = new JMenuItem();
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377 JMenuItem eps = new JMenuItem();
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378 JMenuItem mapping = new JMenuItem();
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379 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
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380 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
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381 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
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382 JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
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384 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
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385 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
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386 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
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387 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
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388 JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
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389 JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
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390 JRadioButtonMenuItem user = new JRadioButtonMenuItem();
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391 JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
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392 JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
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393 JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
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394 JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
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395 JMenu viewMenu = new JMenu();
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396 JMenuItem background = new JMenuItem();
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401 * @param e DOCUMENT ME!
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403 public void eps_actionPerformed(ActionEvent e)
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405 makePDBImage(jalview.util.ImageMaker.EPS);
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411 * @param e DOCUMENT ME!
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413 public void png_actionPerformed(ActionEvent e)
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415 makePDBImage(jalview.util.ImageMaker.PNG);
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418 void makePDBImage(int type)
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420 int width = pdbcanvas.getWidth();
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421 int height = pdbcanvas.getHeight();
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423 jalview.util.ImageMaker im;
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425 if (type == jalview.util.ImageMaker.PNG)
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426 im = new jalview.util.ImageMaker(this,
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427 jalview.util.ImageMaker.PNG,
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428 "Make PNG image from view",
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432 im = new jalview.util.ImageMaker(this,
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433 jalview.util.ImageMaker.EPS,
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434 "Make EPS file from view",
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436 null, this.getTitle());
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438 if (im.getGraphics() != null)
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440 pdbcanvas.drawAll(im.getGraphics(), width, height);
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444 public void charge_actionPerformed(ActionEvent e)
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446 pdbcanvas.bysequence = false;
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447 pdbcanvas.pdb.setChargeColours();
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448 pdbcanvas.redrawneeded=true;
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449 pdbcanvas.repaint();
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452 public void hydro_actionPerformed(ActionEvent e)
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454 pdbcanvas.bysequence = false;
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455 pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
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456 pdbcanvas.redrawneeded=true;
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457 pdbcanvas.repaint();
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460 public void chain_actionPerformed(ActionEvent e)
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462 pdbcanvas.bysequence = false;
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463 pdbcanvas.pdb.setChainColours();
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464 pdbcanvas.redrawneeded=true;
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465 pdbcanvas.repaint();
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468 public void zbuffer_actionPerformed(ActionEvent e)
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470 pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
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471 pdbcanvas.redrawneeded=true;
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472 pdbcanvas.repaint();
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475 public void molecule_actionPerformed(ActionEvent e)
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477 pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
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478 pdbcanvas.redrawneeded=true;
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479 pdbcanvas.repaint();
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482 public void depth_actionPerformed(ActionEvent e)
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484 pdbcanvas.depthcue = ! pdbcanvas.depthcue;
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485 pdbcanvas.redrawneeded=true;
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486 pdbcanvas.repaint();
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489 public void wire_actionPerformed(ActionEvent e)
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491 pdbcanvas.wire = ! pdbcanvas.wire;
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492 pdbcanvas.redrawneeded=true;
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493 pdbcanvas.repaint();
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496 public void seqButton_actionPerformed(ActionEvent e)
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498 pdbcanvas.bysequence = true;
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499 pdbcanvas.updateSeqColours();
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503 public void mapping_actionPerformed(ActionEvent e)
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505 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
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506 Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
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507 cap.setText(pdbcanvas.mappingDetails.toString());
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510 public void allchains_itemStateChanged(ItemEvent e)
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512 pdbcanvas.setAllchainsVisible(allchains.getState());
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514 void showErrorMessage(String error)
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516 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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517 error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
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521 public void zappo_actionPerformed(ActionEvent e)
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523 pdbcanvas.bysequence = false;
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524 pdbcanvas.pdb.setColours(new ZappoColourScheme());
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525 pdbcanvas.redrawneeded=true;
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526 pdbcanvas.repaint();
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529 public void taylor_actionPerformed(ActionEvent e)
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531 pdbcanvas.bysequence = false;
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532 pdbcanvas.pdb.setColours(new TaylorColourScheme());
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533 pdbcanvas.redrawneeded=true;
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534 pdbcanvas.repaint();
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537 public void helix_actionPerformed(ActionEvent e)
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539 pdbcanvas.bysequence = false;
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540 pdbcanvas.pdb.setColours(new HelixColourScheme());
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541 pdbcanvas.redrawneeded=true;
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542 pdbcanvas.repaint();
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545 public void strand_actionPerformed(ActionEvent e)
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547 pdbcanvas.bysequence = false;
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548 pdbcanvas.pdb.setColours(new StrandColourScheme());
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549 pdbcanvas.redrawneeded=true;
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550 pdbcanvas.repaint();
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553 public void turn_actionPerformed(ActionEvent e)
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555 pdbcanvas.bysequence = false;
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556 pdbcanvas.pdb.setColours(new TurnColourScheme());
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557 pdbcanvas.redrawneeded=true;
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558 pdbcanvas.repaint();
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561 public void buried_actionPerformed(ActionEvent e)
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563 pdbcanvas.bysequence = false;
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564 pdbcanvas.pdb.setColours(new BuriedColourScheme());
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565 pdbcanvas.redrawneeded=true;
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566 pdbcanvas.repaint();
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569 public void user_actionPerformed(ActionEvent e)
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571 if (e.getActionCommand().equals("User Defined..."))
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573 new UserDefinedColours(pdbcanvas, null);
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577 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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578 getUserColourSchemes().get(e.getActionCommand());
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580 pdbcanvas.pdb.setColours(udc);
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581 pdbcanvas.redrawneeded=true;
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582 pdbcanvas.repaint();
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586 public void background_actionPerformed(ActionEvent e)
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588 java.awt.Color col = JColorChooser.showDialog(this, "Select Background Colour",
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589 pdbcanvas.backgroundColour);
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593 pdbcanvas.backgroundColour = col;
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594 pdbcanvas.redrawneeded = true;
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595 pdbcanvas.repaint();
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