3 import javax.swing.*;
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4 import java.awt.event.*;
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5 import jalview.datamodel.*;
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6 import jalview.gui.*;
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7 import jalview.io.EBIFetchClient;
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8 import java.awt.event.ActionListener;
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9 import java.awt.event.ActionEvent;
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11 public class PDBViewer extends JInternalFrame implements Runnable
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15 PDBCanvas pdbcanvas;
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18 public PDBViewer(PDBEntry entry,
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20 SeqCanvas seqcanvas)
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29 catch (Exception ex)
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31 ex.printStackTrace();
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34 pdbcanvas = new PDBCanvas(seqcanvas, seq);
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36 setContentPane(pdbcanvas);
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37 StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
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38 if(pdb.getProperty()!=null)
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40 title.append( " Method: " );
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41 title.append(pdb.getProperty().get("method"));
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42 title.append( " Chain:" );
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43 title.append( pdb.getProperty().get("chains"));
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45 Desktop.addInternalFrame(this,title.toString(),400, 400);
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47 Thread worker = new Thread(this);
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55 EBIFetchClient ebi = new EBIFetchClient();
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56 String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,
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59 PDBfile pdbfile = new PDBfile(result);
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61 pdbcanvas.setPDBFile(pdbfile);
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64 catch (Exception ex)
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66 ex.printStackTrace();
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70 private void jbInit()
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73 this.addKeyListener(new KeyAdapter()
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75 public void keyPressed(KeyEvent evt)
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77 pdbcanvas.keyPressed(evt);
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81 this.setJMenuBar(jMenuBar1);
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82 fileMenu.setText("File");
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83 coloursMenu.setText("Colours");
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84 saveMenu.setActionCommand("Save Image");
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85 saveMenu.setText("Save As");
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87 png.addActionListener(new ActionListener()
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89 public void actionPerformed(ActionEvent e)
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91 png_actionPerformed(e);
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95 eps.addActionListener(new ActionListener()
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97 public void actionPerformed(ActionEvent e)
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99 eps_actionPerformed(e);
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102 mapping.setText("View Mapping");
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103 mapping.addActionListener(new ActionListener()
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105 public void actionPerformed(ActionEvent e)
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107 mapping_actionPerformed(e);
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110 wire.setText("Wireframe");
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111 wire.addActionListener(new ActionListener()
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113 public void actionPerformed(ActionEvent e)
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115 wire_actionPerformed(e);
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118 depth.setSelected(true);
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119 depth.setText("Depthcue");
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120 depth.addActionListener(new ActionListener()
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122 public void actionPerformed(ActionEvent e)
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124 depth_actionPerformed(e);
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127 zbuffer.setSelected(true);
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128 zbuffer.setText("Z Buffering");
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129 zbuffer.addActionListener(new ActionListener()
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131 public void actionPerformed(ActionEvent e)
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133 zbuffer_actionPerformed(e);
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136 charge.setText("Charge & Cysteine");
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137 charge.addActionListener(new ActionListener()
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139 public void actionPerformed(ActionEvent e)
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141 charge_actionPerformed(e);
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144 hydro.setText("Hydrophobicity");
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145 hydro.addActionListener(new ActionListener()
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147 public void actionPerformed(ActionEvent e)
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149 hydro_actionPerformed(e);
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152 chain.setText("By Chain");
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153 chain.addActionListener(new ActionListener()
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155 public void actionPerformed(ActionEvent e)
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157 chain_actionPerformed(e);
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160 seqButton.setSelected(true);
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161 seqButton.setText("By Sequence");
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162 seqButton.addActionListener(new ActionListener()
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164 public void actionPerformed(ActionEvent e)
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166 seqButton_actionPerformed(e);
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169 molecule.setText("By Molecule");
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170 molecule.addActionListener(new ActionListener()
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172 public void actionPerformed(ActionEvent e)
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174 molecule_actionPerformed(e);
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177 jMenuBar1.add(fileMenu);
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178 jMenuBar1.add(coloursMenu);
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179 fileMenu.add(saveMenu);
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180 fileMenu.add(mapping);
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183 coloursMenu.add(seqButton);
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184 coloursMenu.add(chain);
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185 coloursMenu.add(hydro);
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186 coloursMenu.add(charge);
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187 coloursMenu.addSeparator();
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188 coloursMenu.add(wire);
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189 coloursMenu.add(depth);
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190 coloursMenu.add(zbuffer);
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191 coloursMenu.add(molecule);
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192 ButtonGroup bg = new ButtonGroup();
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199 JMenuBar jMenuBar1 = new JMenuBar();
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200 JMenu fileMenu = new JMenu();
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201 JMenu coloursMenu = new JMenu();
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202 JMenu saveMenu = new JMenu();
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203 JMenuItem png = new JMenuItem();
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204 JMenuItem eps = new JMenuItem();
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205 JMenuItem mapping = new JMenuItem();
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206 JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
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207 JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
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208 JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
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209 JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
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210 JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
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211 JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
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212 JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
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213 JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();
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218 * @param e DOCUMENT ME!
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220 public void eps_actionPerformed(ActionEvent e)
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222 makePDBImage(jalview.util.ImageMaker.EPS);
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228 * @param e DOCUMENT ME!
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230 public void png_actionPerformed(ActionEvent e)
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232 makePDBImage(jalview.util.ImageMaker.PNG);
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235 void makePDBImage(int type)
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237 int width = pdbcanvas.getWidth();
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238 int height = pdbcanvas.getHeight();
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240 jalview.util.ImageMaker im;
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242 if (type == jalview.util.ImageMaker.PNG)
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243 im = new jalview.util.ImageMaker(this,
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244 jalview.util.ImageMaker.PNG,
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245 "Make PNG image from view",
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249 im = new jalview.util.ImageMaker(this,
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250 jalview.util.ImageMaker.EPS,
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251 "Make EPS file from view",
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253 null, this.getTitle());
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255 if (im.getGraphics() != null)
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257 pdbcanvas.drawAll(im.getGraphics(), width, height);
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261 public void charge_actionPerformed(ActionEvent e)
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263 clearButtonGroup();
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264 pdbcanvas.pdb.setChargeColours();
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265 pdbcanvas.redrawneeded=true;
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266 pdbcanvas.repaint();
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269 public void hydro_actionPerformed(ActionEvent e)
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271 clearButtonGroup();
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272 pdbcanvas.pdb.setHydrophobicityColours();
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273 pdbcanvas.redrawneeded=true;
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274 pdbcanvas.repaint();
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277 public void chain_actionPerformed(ActionEvent e)
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279 clearButtonGroup();
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280 pdbcanvas.pdb.setChainColours();
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281 pdbcanvas.redrawneeded=true;
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282 pdbcanvas.repaint();
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285 public void zbuffer_actionPerformed(ActionEvent e)
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287 pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
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288 pdbcanvas.redrawneeded=true;
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289 pdbcanvas.repaint();
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292 public void molecule_actionPerformed(ActionEvent e)
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294 pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
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295 pdbcanvas.redrawneeded=true;
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296 pdbcanvas.repaint();
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299 public void depth_actionPerformed(ActionEvent e)
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301 pdbcanvas.depthcue = ! pdbcanvas.depthcue;
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302 pdbcanvas.redrawneeded=true;
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303 pdbcanvas.repaint();
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306 public void wire_actionPerformed(ActionEvent e)
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308 pdbcanvas.wire = ! pdbcanvas.wire;
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309 pdbcanvas.redrawneeded=true;
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310 pdbcanvas.repaint();
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313 public void seqButton_actionPerformed(ActionEvent e)
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315 clearButtonGroup();
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316 pdbcanvas.bysequence = seqButton.isSelected();
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317 pdbcanvas.updateSeqColours();
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320 void clearButtonGroup()
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322 pdbcanvas.bysequence = false;
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323 pdbcanvas.bymolecule = false;
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326 public void mapping_actionPerformed(ActionEvent e)
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328 jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
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329 Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 500, 600);
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330 cap.setText(pdbcanvas.mappingDetails.toString());
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