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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55 Thread worker = new Thread(this);
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58 pdbcanvas = new PDBCanvas(seqcanvas, seq);
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60 setContentPane(pdbcanvas);
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61 StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
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62 if(pdb.getProperty()!=null)
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64 title.append( " Method: " );
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65 title.append(pdb.getProperty().get("method"));
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66 title.append( " Chain:" );
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67 title.append( pdb.getProperty().get("chains"));
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70 Desktop.addInternalFrame(this,title.toString(),400, 400);
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77 EBIFetchClient ebi = new EBIFetchClient();
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78 String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");
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80 PDBfile pdbfile = new PDBfile(result);
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82 pdbcanvas.setPDBFile(pdbfile);
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88 catch (Exception ex)
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90 ex.printStackTrace();
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93 catch (Exception ex)
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95 ex.printStackTrace();
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99 private void jbInit()
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102 this.addKeyListener(new KeyAdapter()
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104 public void keyPressed(KeyEvent evt)
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106 pdbcanvas.keyPressed(evt);
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110 this.setJMenuBar(jMenuBar1);
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111 fileMenu.setText("File");
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112 coloursMenu.setText("Colours");
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113 saveMenu.setActionCommand("Save Image");
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114 saveMenu.setText("Save As");
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115 png.setText("PNG");
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116 png.addActionListener(new ActionListener()
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118 public void actionPerformed(ActionEvent e)
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120 png_actionPerformed(e);
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123 eps.setText("EPS");
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124 eps.addActionListener(new ActionListener()
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126 public void actionPerformed(ActionEvent e)
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128 eps_actionPerformed(e);
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131 mapping.setText("View Mapping");
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132 mapping.addActionListener(new ActionListener()
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134 public void actionPerformed(ActionEvent e)
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136 mapping_actionPerformed(e);
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139 wire.setText("Wireframe");
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140 wire.addActionListener(new ActionListener()
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142 public void actionPerformed(ActionEvent e)
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144 wire_actionPerformed(e);
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147 depth.setSelected(true);
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148 depth.setText("Depthcue");
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149 depth.addActionListener(new ActionListener()
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151 public void actionPerformed(ActionEvent e)
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153 depth_actionPerformed(e);
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156 zbuffer.setSelected(true);
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157 zbuffer.setText("Z Buffering");
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158 zbuffer.addActionListener(new ActionListener()
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160 public void actionPerformed(ActionEvent e)
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162 zbuffer_actionPerformed(e);
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165 charge.setText("Charge & Cysteine");
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166 charge.addActionListener(new ActionListener()
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168 public void actionPerformed(ActionEvent e)
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170 charge_actionPerformed(e);
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173 chain.setText("By Chain");
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174 chain.addActionListener(new ActionListener()
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176 public void actionPerformed(ActionEvent e)
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178 chain_actionPerformed(e);
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181 seqButton.setSelected(true);
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182 seqButton.setText("By Sequence");
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183 seqButton.addActionListener(new ActionListener()
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185 public void actionPerformed(ActionEvent e)
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187 seqButton_actionPerformed(e);
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190 allchains.setSelected(true);
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191 allchains.setText("Show All Chains");
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192 allchains.addItemListener(new ItemListener()
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194 public void itemStateChanged(ItemEvent e)
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196 allchains_itemStateChanged(e);
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199 zappo.setText("Zappo");
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200 zappo.addActionListener(new ActionListener()
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202 public void actionPerformed(ActionEvent e)
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204 zappo_actionPerformed(e);
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207 taylor.setText("Taylor");
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208 taylor.addActionListener(new ActionListener()
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210 public void actionPerformed(ActionEvent e)
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212 taylor_actionPerformed(e);
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215 hydro.setText("Hydro");
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216 hydro.addActionListener(new ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 hydro_actionPerformed(e);
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223 helix.setText("Helix");
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224 helix.addActionListener(new ActionListener()
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226 public void actionPerformed(ActionEvent e)
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228 helix_actionPerformed(e);
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231 strand.setText("Strand");
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232 strand.addActionListener(new ActionListener()
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234 public void actionPerformed(ActionEvent e)
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236 strand_actionPerformed(e);
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239 turn.setText("Turn");
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240 turn.addActionListener(new ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 turn_actionPerformed(e);
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247 buried.setText("Buried");
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248 buried.addActionListener(new ActionListener()
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250 public void actionPerformed(ActionEvent e)
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252 buried_actionPerformed(e);
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255 user.setText("User Defined...");
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256 user.addActionListener(new ActionListener()
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258 public void actionPerformed(ActionEvent e)
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260 user_actionPerformed(e);
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263 viewMenu.setText("View");
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264 jMenuBar1.add(fileMenu);
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265 jMenuBar1.add(coloursMenu);
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266 jMenuBar1.add(viewMenu);
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267 fileMenu.add(saveMenu);
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268 fileMenu.add(mapping);
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271 coloursMenu.add(seqButton);
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272 coloursMenu.add(chain);
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273 coloursMenu.add(charge);
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274 coloursMenu.add(zappo);
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275 coloursMenu.add(taylor);
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276 coloursMenu.add(hydro);
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277 coloursMenu.add(helix);
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278 coloursMenu.add(strand);
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279 coloursMenu.add(turn);
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280 coloursMenu.add(buried);
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281 coloursMenu.add(user);
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282 ButtonGroup bg = new ButtonGroup();
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296 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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298 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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299 getUserColourSchemes().keys();
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301 while (userColours.hasMoreElements())
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303 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
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304 nextElement().toString());
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305 radioItem.setName("USER_DEFINED");
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306 radioItem.addMouseListener(new MouseAdapter()
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308 public void mousePressed(MouseEvent evt)
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310 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
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312 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
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314 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
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315 "Remove from default list?",
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316 "Remove user defined colour",
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317 JOptionPane.YES_NO_OPTION);
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318 if(option == JOptionPane.YES_OPTION)
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320 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
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321 coloursMenu.remove(radioItem);
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324 radioItem.addActionListener(new ActionListener()
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326 public void actionPerformed(ActionEvent evt)
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328 user_actionPerformed(evt);
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334 radioItem.addActionListener(new ActionListener()
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336 public void actionPerformed(ActionEvent evt)
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338 user_actionPerformed(evt);
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341 coloursMenu.add(radioItem);
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346 viewMenu.add(wire);
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347 viewMenu.add(depth);
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348 viewMenu.add(zbuffer);
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349 viewMenu.add(allchains);
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352 JMenuBar jMenuBar1 = new JMenuBar();
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353 JMenu fileMenu = new JMenu();
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354 JMenu coloursMenu = new JMenu();
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355 JMenu saveMenu = new JMenu();
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356 JMenuItem png = new JMenuItem();
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357 JMenuItem eps = new JMenuItem();
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358 JMenuItem mapping = new JMenuItem();
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359 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
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360 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
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361 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
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362 JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
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364 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
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365 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
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366 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
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367 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
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368 JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
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369 JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
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370 JRadioButtonMenuItem user = new JRadioButtonMenuItem();
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371 JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
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372 JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
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373 JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
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374 JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
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375 JMenu viewMenu = new JMenu();
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380 * @param e DOCUMENT ME!
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382 public void eps_actionPerformed(ActionEvent e)
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384 makePDBImage(jalview.util.ImageMaker.EPS);
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390 * @param e DOCUMENT ME!
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392 public void png_actionPerformed(ActionEvent e)
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394 makePDBImage(jalview.util.ImageMaker.PNG);
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397 void makePDBImage(int type)
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399 int width = pdbcanvas.getWidth();
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400 int height = pdbcanvas.getHeight();
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402 jalview.util.ImageMaker im;
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404 if (type == jalview.util.ImageMaker.PNG)
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405 im = new jalview.util.ImageMaker(this,
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406 jalview.util.ImageMaker.PNG,
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407 "Make PNG image from view",
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411 im = new jalview.util.ImageMaker(this,
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412 jalview.util.ImageMaker.EPS,
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413 "Make EPS file from view",
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415 null, this.getTitle());
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417 if (im.getGraphics() != null)
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419 pdbcanvas.drawAll(im.getGraphics(), width, height);
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423 public void charge_actionPerformed(ActionEvent e)
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425 pdbcanvas.bysequence = false;
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426 pdbcanvas.pdb.setChargeColours();
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427 pdbcanvas.redrawneeded=true;
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428 pdbcanvas.repaint();
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431 public void hydro_actionPerformed(ActionEvent e)
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433 pdbcanvas.bysequence = false;
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434 pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
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435 pdbcanvas.redrawneeded=true;
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436 pdbcanvas.repaint();
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439 public void chain_actionPerformed(ActionEvent e)
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441 pdbcanvas.bysequence = false;
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442 pdbcanvas.pdb.setChainColours();
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443 pdbcanvas.redrawneeded=true;
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444 pdbcanvas.repaint();
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447 public void zbuffer_actionPerformed(ActionEvent e)
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449 pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
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450 pdbcanvas.redrawneeded=true;
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451 pdbcanvas.repaint();
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454 public void molecule_actionPerformed(ActionEvent e)
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456 pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
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457 pdbcanvas.redrawneeded=true;
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458 pdbcanvas.repaint();
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461 public void depth_actionPerformed(ActionEvent e)
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463 pdbcanvas.depthcue = ! pdbcanvas.depthcue;
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464 pdbcanvas.redrawneeded=true;
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465 pdbcanvas.repaint();
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468 public void wire_actionPerformed(ActionEvent e)
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470 pdbcanvas.wire = ! pdbcanvas.wire;
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471 pdbcanvas.redrawneeded=true;
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472 pdbcanvas.repaint();
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475 public void seqButton_actionPerformed(ActionEvent e)
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477 pdbcanvas.bysequence = true;
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478 pdbcanvas.updateSeqColours();
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482 public void mapping_actionPerformed(ActionEvent e)
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484 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
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485 Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
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486 cap.setText(pdbcanvas.mappingDetails.toString());
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489 public void allchains_itemStateChanged(ItemEvent e)
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491 pdbcanvas.setAllchainsVisible(allchains.getState());
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494 public void zappo_actionPerformed(ActionEvent e)
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496 pdbcanvas.bysequence = false;
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497 pdbcanvas.pdb.setColours(new ZappoColourScheme());
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498 pdbcanvas.redrawneeded=true;
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499 pdbcanvas.repaint();
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502 public void taylor_actionPerformed(ActionEvent e)
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504 pdbcanvas.bysequence = false;
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505 pdbcanvas.pdb.setColours(new TaylorColourScheme());
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506 pdbcanvas.redrawneeded=true;
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507 pdbcanvas.repaint();
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510 public void helix_actionPerformed(ActionEvent e)
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512 pdbcanvas.bysequence = false;
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513 pdbcanvas.pdb.setColours(new HelixColourScheme());
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514 pdbcanvas.redrawneeded=true;
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515 pdbcanvas.repaint();
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518 public void strand_actionPerformed(ActionEvent e)
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520 pdbcanvas.bysequence = false;
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521 pdbcanvas.pdb.setColours(new StrandColourScheme());
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522 pdbcanvas.redrawneeded=true;
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523 pdbcanvas.repaint();
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526 public void turn_actionPerformed(ActionEvent e)
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528 pdbcanvas.bysequence = false;
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529 pdbcanvas.pdb.setColours(new TurnColourScheme());
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530 pdbcanvas.redrawneeded=true;
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531 pdbcanvas.repaint();
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534 public void buried_actionPerformed(ActionEvent e)
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536 pdbcanvas.bysequence = false;
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537 pdbcanvas.pdb.setColours(new BuriedColourScheme());
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538 pdbcanvas.redrawneeded=true;
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539 pdbcanvas.repaint();
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542 public void user_actionPerformed(ActionEvent e)
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544 if (e.getActionCommand().equals("User Defined..."))
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546 new UserDefinedColours(pdbcanvas, null);
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550 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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551 getUserColourSchemes().get(e.getActionCommand());
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553 pdbcanvas.pdb.setColours(udc);
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554 pdbcanvas.redrawneeded=true;
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555 pdbcanvas.repaint();
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