2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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22 import java.awt.event.*;
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24 import jalview.appletgui.*;
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25 import jalview.datamodel.*;
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26 import jalview.schemes.*;
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29 public class AppletPDBViewer
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30 extends Frame implements ActionListener, ItemListener
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32 AppletPDBCanvas pdbcanvas;
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34 public AppletPDBViewer(PDBEntry pdbentry,
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44 catch (Exception ex)
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46 ex.printStackTrace();
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49 pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);
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52 add(pdbcanvas, BorderLayout.CENTER);
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54 StringBuffer title = new StringBuffer(seq[0].getName()
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56 + pdbcanvas.pdbentry.getFile());
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58 jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
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64 public void actionPerformed(ActionEvent evt)
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66 if (evt.getSource() == mapping)
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68 jalview.appletgui.CutAndPasteTransfer cap
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69 = new jalview.appletgui.CutAndPasteTransfer(false, null);
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70 Frame frame = new Frame();
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72 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,
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74 cap.setText(pdbcanvas.mappingDetails.toString());
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77 else if (evt.getSource() == charge)
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79 pdbcanvas.bysequence = false;
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80 pdbcanvas.pdb.setChargeColours();
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83 else if (evt.getSource() == chain)
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85 pdbcanvas.bysequence = false;
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86 pdbcanvas.pdb.setChainColours();
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88 else if (evt.getSource() == seqButton)
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90 pdbcanvas.bysequence = true;
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91 pdbcanvas.colourBySequence();
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94 else if (evt.getSource() == zappo)
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96 pdbcanvas.setColours(new ZappoColourScheme());
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98 else if (evt.getSource() == taylor)
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100 pdbcanvas.setColours(new TaylorColourScheme());
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102 else if (evt.getSource() == hydro)
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104 pdbcanvas.setColours(new HydrophobicColourScheme());
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106 else if (evt.getSource() == helix)
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108 pdbcanvas.setColours(new HelixColourScheme());
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110 else if (evt.getSource() == strand)
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112 pdbcanvas.setColours(new StrandColourScheme());
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114 else if (evt.getSource() == turn)
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116 pdbcanvas.setColours(new TurnColourScheme());
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118 else if (evt.getSource() == buried)
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120 pdbcanvas.setColours(new BuriedColourScheme());
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122 else if (evt.getSource() == user)
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124 pdbcanvas.bysequence = false;
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125 new jalview.appletgui.UserDefinedColours(pdbcanvas);
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128 pdbcanvas.redrawneeded = true;
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129 pdbcanvas.repaint();
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133 public void itemStateChanged(ItemEvent evt)
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135 if (evt.getSource() == allchains)
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137 pdbcanvas.setAllchainsVisible(allchains.getState());
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139 else if (evt.getSource() == wire)
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141 pdbcanvas.wire = !pdbcanvas.wire;
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143 else if (evt.getSource() == depth)
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145 pdbcanvas.depthcue = !pdbcanvas.depthcue;
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147 else if (evt.getSource() == zbuffer)
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149 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
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151 pdbcanvas.redrawneeded = true;
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152 pdbcanvas.repaint();
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155 private void jbInit()
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158 setMenuBar(jMenuBar1);
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159 fileMenu.setLabel("File");
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160 coloursMenu.setLabel("Colours");
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161 mapping.setLabel("View Mapping");
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162 mapping.addActionListener(this);
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163 wire.setLabel("Wireframe");
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164 wire.addItemListener(this);
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165 depth.setState(true);
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166 depth.setLabel("Depthcue");
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167 depth.addItemListener(this);
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168 zbuffer.setState(true);
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169 zbuffer.setLabel("Z Buffering");
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170 zbuffer.addItemListener(this);
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171 charge.setLabel("Charge & Cysteine");
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172 charge.addActionListener(this);
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173 hydro.setLabel("Hydrophobicity");
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174 hydro.addActionListener(this);
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175 chain.setLabel("By Chain");
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176 chain.addActionListener(this);
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177 seqButton.setLabel("By Sequence");
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178 seqButton.addActionListener(this);
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179 allchains.setLabel("All Chains Visible");
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180 allchains.addItemListener(this);
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181 viewMenu.setLabel("View");
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182 zappo.setLabel("Zappo");
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183 zappo.addActionListener(this);
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184 taylor.setLabel("Taylor");
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185 taylor.addActionListener(this);
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186 helix.setLabel("Helix Propensity");
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187 helix.addActionListener(this);
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188 strand.setLabel("Strand Propensity");
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189 strand.addActionListener(this);
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190 turn.setLabel("Turn Propensity");
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191 turn.addActionListener(this);
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192 buried.setLabel("Buried Index");
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193 buried.addActionListener(this);
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194 user.setLabel("User Defined...");
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195 user.addActionListener(this);
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196 jMenuBar1.add(fileMenu);
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197 jMenuBar1.add(coloursMenu);
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198 jMenuBar1.add(viewMenu);
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199 fileMenu.add(mapping); ;
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201 coloursMenu.add(seqButton);
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202 coloursMenu.add(chain);
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203 coloursMenu.add(charge);
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204 coloursMenu.add(zappo);
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205 coloursMenu.add(taylor);
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206 coloursMenu.add(hydro);
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207 coloursMenu.add(helix);
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208 coloursMenu.add(strand);
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209 coloursMenu.add(turn);
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210 coloursMenu.add(buried);
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211 coloursMenu.add(user);
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212 viewMenu.add(wire);
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213 viewMenu.add(depth);
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214 viewMenu.add(zbuffer);
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215 viewMenu.add(allchains);
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216 allchains.setState(true);
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219 MenuBar jMenuBar1 = new MenuBar();
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220 Menu fileMenu = new Menu();
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221 Menu coloursMenu = new Menu();
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222 MenuItem mapping = new MenuItem();
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223 CheckboxGroup bg = new CheckboxGroup();
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224 CheckboxMenuItem wire = new CheckboxMenuItem();
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225 CheckboxMenuItem depth = new CheckboxMenuItem();
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226 CheckboxMenuItem zbuffer = new CheckboxMenuItem();
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228 MenuItem charge = new MenuItem();
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229 MenuItem hydro = new MenuItem();
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230 MenuItem chain = new MenuItem();
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231 MenuItem seqButton = new MenuItem();
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233 CheckboxMenuItem allchains = new CheckboxMenuItem();
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234 Menu viewMenu = new Menu();
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235 MenuItem turn = new MenuItem();
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236 MenuItem strand = new MenuItem();
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237 MenuItem helix = new MenuItem();
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238 MenuItem taylor = new MenuItem();
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239 MenuItem zappo = new MenuItem();
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240 MenuItem buried = new MenuItem();
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241 MenuItem user = new MenuItem();
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244 //End StructureListener
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245 ////////////////////////////
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