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 java.awt.event.ActionListener;
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27 import java.awt.event.ActionEvent;
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30 public class AppletPDBViewer extends Frame
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34 AppletPDBCanvas pdbcanvas;
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37 public AppletPDBViewer(String pdbtext,String type,
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39 SeqCanvas seqcanvas)
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47 catch (Exception ex)
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49 ex.printStackTrace();
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52 pdbcanvas = new AppletPDBCanvas(seqcanvas, seq);
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54 add(pdbcanvas, BorderLayout.CENTER);
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56 StringBuffer title = new StringBuffer(sequence.getName() + ":");
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58 jalview.bin.JalviewLite.addFrame(this,title.toString(),400, 400);
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61 PDBfile pdbfile = new PDBfile(pdbtext, type);
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62 pdbcanvas.setPDBFile(pdbfile);
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64 catch(Exception ex){
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65 pdbcanvas.errorLoading = true;
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66 pdbcanvas.repaint();
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71 private void jbInit()
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74 this.setMenuBar(jMenuBar1);
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75 fileMenu.setLabel("File");
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76 coloursMenu.setLabel("Colours");
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77 mapping.setLabel("View Mapping");
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78 mapping.addActionListener(new ActionListener()
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80 public void actionPerformed(ActionEvent e)
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82 mapping_actionPerformed();
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85 wire.setLabel("Wireframe");
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86 wire.addItemListener(new ItemListener()
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88 public void itemStateChanged(ItemEvent e)
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90 wire_actionPerformed();
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93 depth.setState(true);
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94 depth.setLabel("Depthcue");
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95 depth.addItemListener(new ItemListener()
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97 public void itemStateChanged(ItemEvent e)
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99 depth_actionPerformed();
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102 zbuffer.setState(true);
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103 zbuffer.setLabel("Z Buffering");
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104 zbuffer.addItemListener(new ItemListener()
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106 public void itemStateChanged(ItemEvent e)
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108 zbuffer_actionPerformed();
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111 charge.setLabel("Charge & Cysteine");
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112 charge.addActionListener(new ActionListener()
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114 public void actionPerformed(ActionEvent e)
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116 charge_actionPerformed();
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119 hydro.setLabel("Hydrophobicity");
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120 hydro.addActionListener(new ActionListener()
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122 public void actionPerformed(ActionEvent e)
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124 hydro_actionPerformed();
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127 chain.setLabel("By Chain");
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128 chain.addActionListener(new ActionListener()
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130 public void actionPerformed(ActionEvent e)
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132 chain_actionPerformed();
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135 seqButton.setLabel("By Sequence");
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136 seqButton.addActionListener(new ActionListener()
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138 public void actionPerformed(ActionEvent e){
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139 seqButton_actionPerformed();
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142 allchains.setLabel("All Chains Visible");
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143 allchains.addItemListener(new ItemListener()
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145 public void itemStateChanged(ItemEvent itemEvent)
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147 allchains_itemStateChanged(itemEvent);
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150 jMenuBar1.add(fileMenu);
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151 jMenuBar1.add(coloursMenu);
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152 fileMenu.add(mapping);;
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154 coloursMenu.add(seqButton);
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155 coloursMenu.add(chain);
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156 coloursMenu.add(hydro);
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157 coloursMenu.add(charge);
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158 coloursMenu.addSeparator();
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159 coloursMenu.add(wire);
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160 coloursMenu.add(depth);
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161 coloursMenu.add(zbuffer);
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162 coloursMenu.add(allchains);
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163 allchains.setState(true);
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166 MenuBar jMenuBar1 = new MenuBar();
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167 Menu fileMenu = new Menu();
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168 Menu coloursMenu = new Menu();
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169 MenuItem mapping = new MenuItem();
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170 CheckboxGroup bg = new CheckboxGroup();
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171 CheckboxMenuItem wire = new CheckboxMenuItem();
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172 CheckboxMenuItem depth = new CheckboxMenuItem();
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173 CheckboxMenuItem zbuffer = new CheckboxMenuItem();
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175 MenuItem charge = new MenuItem();
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176 MenuItem hydro = new MenuItem();
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177 MenuItem chain = new MenuItem();
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178 MenuItem seqButton = new MenuItem();
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180 CheckboxMenuItem allchains = new CheckboxMenuItem();
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182 public void charge_actionPerformed()
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184 clearButtonGroup();
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185 pdbcanvas.pdb.setChargeColours();
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186 pdbcanvas.redrawneeded=true;
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187 pdbcanvas.repaint();
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190 public void hydro_actionPerformed()
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192 clearButtonGroup();
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193 // pdbcanvas.pdb.setHydrophobicityColours();
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194 pdbcanvas.redrawneeded=true;
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195 pdbcanvas.repaint();
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198 public void chain_actionPerformed()
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200 clearButtonGroup();
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201 pdbcanvas.pdb.setChainColours();
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202 pdbcanvas.redrawneeded=true;
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203 pdbcanvas.repaint();
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206 public void zbuffer_actionPerformed()
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208 pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
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209 pdbcanvas.redrawneeded=true;
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210 pdbcanvas.repaint();
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213 public void depth_actionPerformed()
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215 pdbcanvas.depthcue = ! pdbcanvas.depthcue;
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216 pdbcanvas.redrawneeded=true;
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217 pdbcanvas.repaint();
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220 public void wire_actionPerformed()
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222 pdbcanvas.wire = ! pdbcanvas.wire;
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223 pdbcanvas.redrawneeded=true;
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224 pdbcanvas.repaint();
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227 public void seqButton_actionPerformed()
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229 clearButtonGroup();
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230 pdbcanvas.bysequence = true;
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231 pdbcanvas.updateSeqColours();
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232 pdbcanvas.repaint();
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235 void clearButtonGroup()
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237 pdbcanvas.bysequence = false;
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238 pdbcanvas.bymolecule = false;
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241 public void mapping_actionPerformed()
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243 jalview.appletgui.CutAndPasteTransfer cap
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244 = new jalview.appletgui.CutAndPasteTransfer(false, null);
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245 Frame frame = new Frame();
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247 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);
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248 cap.setText(pdbcanvas.mappingDetails.toString());
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251 public void allchains_itemStateChanged(ItemEvent itemEvent)
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253 pdbcanvas.setAllchainsVisible(allchains.getState());
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