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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23 import java.awt.event.*;
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24 import jalview.datamodel.*;
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25 import jalview.appletgui.*;
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26 import jalview.schemes.*;
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27 import java.awt.event.ActionListener;
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28 import java.awt.event.ActionEvent;
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31 public class AppletPDBViewer extends Frame
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35 AppletPDBCanvas pdbcanvas;
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38 public AppletPDBViewer(String pdbtext,String type,
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40 SeqCanvas seqcanvas)
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48 catch (Exception ex)
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50 ex.printStackTrace();
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53 pdbcanvas = new AppletPDBCanvas(seqcanvas, seq);
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55 add(pdbcanvas, BorderLayout.CENTER);
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57 StringBuffer title = new StringBuffer(sequence.getName() + ":");
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59 jalview.bin.JalviewLite.addFrame(this,title.toString(),400, 400);
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62 PDBfile pdbfile = new PDBfile(pdbtext, type);
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63 pdbcanvas.setPDBFile(pdbfile);
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65 catch(Exception ex){
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66 pdbcanvas.errorLoading = true;
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67 pdbcanvas.repaint();
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72 private void jbInit()
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75 this.setMenuBar(jMenuBar1);
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76 fileMenu.setLabel("File");
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77 coloursMenu.setLabel("Colours");
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78 mapping.setLabel("View Mapping");
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79 mapping.addActionListener(new ActionListener()
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81 public void actionPerformed(ActionEvent e)
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83 mapping_actionPerformed();
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86 wire.setLabel("Wireframe");
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87 wire.addItemListener(new ItemListener()
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89 public void itemStateChanged(ItemEvent e)
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91 wire_actionPerformed();
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94 depth.setState(true);
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95 depth.setLabel("Depthcue");
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96 depth.addItemListener(new ItemListener()
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98 public void itemStateChanged(ItemEvent e)
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100 depth_actionPerformed();
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103 zbuffer.setState(true);
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104 zbuffer.setLabel("Z Buffering");
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105 zbuffer.addItemListener(new ItemListener()
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107 public void itemStateChanged(ItemEvent e)
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109 zbuffer_actionPerformed();
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112 charge.setLabel("Charge & Cysteine");
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113 charge.addActionListener(new ActionListener()
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115 public void actionPerformed(ActionEvent e)
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117 charge_actionPerformed();
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120 hydro.setLabel("Hydrophobicity");
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121 hydro.addActionListener(new ActionListener()
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123 public void actionPerformed(ActionEvent e)
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125 pdbcanvas.setColours(new HydrophobicColourScheme());
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128 chain.setLabel("By Chain");
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129 chain.addActionListener(new ActionListener()
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131 public void actionPerformed(ActionEvent e)
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133 chain_actionPerformed();
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136 seqButton.setLabel("By Sequence");
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137 seqButton.addActionListener(new ActionListener()
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139 public void actionPerformed(ActionEvent e){
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140 seqButton_actionPerformed();
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143 allchains.setLabel("All Chains Visible");
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144 allchains.addItemListener(new ItemListener()
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146 public void itemStateChanged(ItemEvent itemEvent)
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148 allchains_itemStateChanged(itemEvent);
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151 viewMenu.setLabel("View");
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152 zappo.setLabel("Zappo");
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153 zappo.addActionListener(new ActionListener()
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155 public void actionPerformed(ActionEvent actionEvent)
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157 pdbcanvas.setColours(new ZappoColourScheme());
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160 taylor.setLabel("Taylor");
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161 taylor.addActionListener(new ActionListener()
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163 public void actionPerformed(ActionEvent actionEvent)
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165 pdbcanvas.setColours(new TaylorColourScheme());
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168 helix.setLabel("Helix Propensity");
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169 helix.addActionListener(new ActionListener()
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171 public void actionPerformed(ActionEvent actionEvent)
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173 pdbcanvas.setColours(new HelixColourScheme());
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176 strand.setLabel("Strand Propensity");
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177 strand.addActionListener(new ActionListener()
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179 public void actionPerformed(ActionEvent actionEvent)
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181 pdbcanvas.setColours(new StrandColourScheme());
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184 turn.setLabel("Turn Propensity");
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185 turn.addActionListener(new ActionListener()
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187 public void actionPerformed(ActionEvent actionEvent)
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189 pdbcanvas.setColours(new TurnColourScheme());
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192 buried.setLabel("Buried Index");
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193 buried.addActionListener(new ActionListener()
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195 public void actionPerformed(ActionEvent actionEvent)
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197 pdbcanvas.setColours(new BuriedColourScheme());
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200 user.setLabel("User Defined...");
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201 user.addActionListener(new ActionListener()
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203 public void actionPerformed(ActionEvent actionEvent)
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205 pdbcanvas.bysequence = false;
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206 new jalview.appletgui.UserDefinedColours(pdbcanvas);
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209 jMenuBar1.add(fileMenu);
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210 jMenuBar1.add(coloursMenu);
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211 jMenuBar1.add(viewMenu);
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212 fileMenu.add(mapping);;
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214 coloursMenu.add(seqButton);
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215 coloursMenu.add(chain);
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216 coloursMenu.add(charge);
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217 coloursMenu.add(zappo);
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218 coloursMenu.add(taylor);
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219 coloursMenu.add(hydro);
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220 coloursMenu.add(helix);
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221 coloursMenu.add(strand);
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222 coloursMenu.add(turn);
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223 coloursMenu.add(buried);
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224 coloursMenu.add(user);
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225 viewMenu.add(wire);
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226 viewMenu.add(depth);
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227 viewMenu.add(zbuffer);
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228 viewMenu.add(allchains);
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229 allchains.setState(true);
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232 MenuBar jMenuBar1 = new MenuBar();
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233 Menu fileMenu = new Menu();
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234 Menu coloursMenu = new Menu();
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235 MenuItem mapping = new MenuItem();
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236 CheckboxGroup bg = new CheckboxGroup();
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237 CheckboxMenuItem wire = new CheckboxMenuItem();
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238 CheckboxMenuItem depth = new CheckboxMenuItem();
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239 CheckboxMenuItem zbuffer = new CheckboxMenuItem();
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241 MenuItem charge = new MenuItem();
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242 MenuItem hydro = new MenuItem();
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243 MenuItem chain = new MenuItem();
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244 MenuItem seqButton = new MenuItem();
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246 CheckboxMenuItem allchains = new CheckboxMenuItem();
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247 Menu viewMenu = new Menu();
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248 MenuItem turn = new MenuItem();
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249 MenuItem strand = new MenuItem();
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250 MenuItem helix = new MenuItem();
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251 MenuItem taylor = new MenuItem();
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252 MenuItem zappo = new MenuItem();
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253 MenuItem buried = new MenuItem();
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254 MenuItem user = new MenuItem();
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256 public void charge_actionPerformed()
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258 pdbcanvas.bysequence = false;
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259 pdbcanvas.pdb.setChargeColours();
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260 pdbcanvas.redrawneeded=true;
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261 pdbcanvas.repaint();
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264 public void chain_actionPerformed()
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266 pdbcanvas.bysequence = false;
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267 pdbcanvas.pdb.setChainColours();
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268 pdbcanvas.redrawneeded=true;
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269 pdbcanvas.repaint();
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272 public void zbuffer_actionPerformed()
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274 pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
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275 pdbcanvas.redrawneeded=true;
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276 pdbcanvas.repaint();
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279 public void depth_actionPerformed()
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281 pdbcanvas.depthcue = ! pdbcanvas.depthcue;
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282 pdbcanvas.redrawneeded=true;
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283 pdbcanvas.repaint();
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286 public void wire_actionPerformed()
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288 pdbcanvas.wire = ! pdbcanvas.wire;
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289 pdbcanvas.redrawneeded=true;
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290 pdbcanvas.repaint();
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293 public void seqButton_actionPerformed()
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295 pdbcanvas.bysequence = true;
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296 pdbcanvas.updateSeqColours();
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297 pdbcanvas.repaint();
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301 public void mapping_actionPerformed()
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303 jalview.appletgui.CutAndPasteTransfer cap
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304 = new jalview.appletgui.CutAndPasteTransfer(false, null);
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305 Frame frame = new Frame();
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307 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);
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308 cap.setText(pdbcanvas.mappingDetails.toString());
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311 public void allchains_itemStateChanged(ItemEvent itemEvent)
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313 pdbcanvas.setAllchainsVisible(allchains.getState());
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