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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19 package jalview.gui;
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22 import java.awt.event.*;
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23 import javax.swing.*;
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26 import jalview.analysis.*;
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27 import jalview.datamodel.*;
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28 import jalview.io.*;
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29 import jalview.schemes.*;
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31 public class PopupMenu
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34 JMenu groupMenu = new JMenu();
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35 JMenuItem groupName = new JMenuItem();
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36 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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37 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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38 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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39 protected JRadioButtonMenuItem hydrophobicityColour = new
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40 JRadioButtonMenuItem();
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41 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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42 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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43 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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44 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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45 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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46 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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47 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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48 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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49 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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50 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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52 JMenu sequenceMenu = new JMenu();
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53 JMenuItem sequenceName = new JMenuItem();
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55 JMenuItem unGroupMenuItem = new JMenuItem();
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56 JMenuItem pdbMenuItem = new JMenuItem();
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57 JMenuItem outline = new JMenuItem();
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58 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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59 JMenu colourMenu = new JMenu();
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60 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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61 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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62 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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64 public PopupMenu(AlignmentPanel ap, Sequence seq)
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66 ///////////////////////////////////////////////////////////
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67 // If this is activated from the sequence panel, the user may want to
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68 // edit or annotate a particular residue. Therefore display the residue menu
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70 // If from the IDPanel, we must display the sequence menu
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71 //////////////////////////////////////////////////////////
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75 ButtonGroup colours = new ButtonGroup();
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76 colours.add(noColourmenuItem);
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77 colours.add(clustalColour);
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78 colours.add(zappoColour);
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79 colours.add(taylorColour);
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80 colours.add(hydrophobicityColour);
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81 colours.add(helixColour);
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82 colours.add(strandColour);
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83 colours.add(turnColour);
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84 colours.add(buriedColour);
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85 colours.add(abovePIDColour);
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86 colours.add(userDefinedColour);
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87 colours.add(PIDColour);
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88 colours.add(BLOSUM62Colour);
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96 e.printStackTrace();
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99 SequenceGroup sg = ap.av.getSelectionGroup();
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103 groupName.setText(sg.getName());
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105 if (sg.cs instanceof ZappoColourScheme)
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107 zappoColour.setSelected(true);
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109 else if (sg.cs instanceof TaylorColourScheme)
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111 taylorColour.setSelected(true);
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113 else if (sg.cs instanceof PIDColourScheme)
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115 PIDColour.setSelected(true);
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117 else if (sg.cs instanceof Blosum62ColourScheme)
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119 BLOSUM62Colour.setSelected(true);
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121 else if (sg.cs instanceof UserColourScheme)
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123 userDefinedColour.setSelected(true);
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125 else if (sg.cs instanceof HydrophobicColourScheme)
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127 hydrophobicityColour.setSelected(true);
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129 else if (sg.cs instanceof HelixColourScheme)
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131 helixColour.setSelected(true);
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133 else if (sg.cs instanceof StrandColourScheme)
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135 strandColour.setSelected(true);
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137 else if (sg.cs instanceof TurnColourScheme)
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139 turnColour.setSelected(true);
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141 else if (sg.cs instanceof BuriedColourScheme)
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143 buriedColour.setSelected(true);
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145 else if (sg.cs instanceof ClustalxColourScheme)
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147 clustalColour.setSelected(true);
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151 noColourmenuItem.setSelected(true);
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154 if (sg.cs instanceof ConservationColourScheme)
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156 conservationMenuItem.setSelected(true);
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159 showText.setSelected(sg.getDisplayText());
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160 showColourText.setSelected(sg.getColourText());
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161 showBoxes.setSelected(sg.getDisplayBoxes());
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164 if (!ap.av.alignment.getGroups().contains(sg))
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166 unGroupMenuItem.setVisible(false);
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170 groupMenu.insertSeparator(3);
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175 sequenceMenu.setVisible(false);
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179 private void jbInit()
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182 groupMenu.setText("Group");
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183 groupMenu.setText("Define");
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184 groupName.setText("Name");
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185 groupName.addActionListener(new java.awt.event.ActionListener()
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187 public void actionPerformed(ActionEvent e)
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189 groupName_actionPerformed(e);
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192 sequenceMenu.setText("Sequence");
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193 sequenceName.setText("Edit name");
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194 sequenceName.addActionListener(new java.awt.event.ActionListener()
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196 public void actionPerformed(ActionEvent e)
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198 sequenceName_actionPerformed(e);
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201 PIDColour.setFocusPainted(false);
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202 unGroupMenuItem.setText("Remove Group");
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203 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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205 public void actionPerformed(ActionEvent e)
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207 unGroupMenuItem_actionPerformed(e);
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210 pdbMenuItem.setText("View PDB structure");
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211 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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213 public void actionPerformed(ActionEvent e)
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215 pdbMenuItem_actionPerformed(e);
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218 outline.setText("Border colour");
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219 outline.addActionListener(new java.awt.event.ActionListener()
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221 public void actionPerformed(ActionEvent e)
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223 outline_actionPerformed(e);
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226 nucleotideMenuItem.setText("Nucleotide");
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227 nucleotideMenuItem.addActionListener(new ActionListener()
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229 public void actionPerformed(ActionEvent e)
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231 nucleotideMenuItem_actionPerformed(e);
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234 colourMenu.setText("Group Colour");
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235 showBoxes.setText("Boxes");
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236 showBoxes.setState(true);
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237 showBoxes.addActionListener(new ActionListener()
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239 public void actionPerformed(ActionEvent e)
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241 showBoxes_actionPerformed(e);
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244 showText.setText("Text");
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245 showText.setState(true);
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246 showText.addActionListener(new ActionListener()
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248 public void actionPerformed(ActionEvent e)
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250 showText_actionPerformed(e);
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253 showColourText.setText("Colour Text");
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254 showColourText.addActionListener(new ActionListener()
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256 public void actionPerformed(ActionEvent e)
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258 showColourText_actionPerformed(e);
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263 groupMenu.add(groupName);
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264 groupMenu.addSeparator();
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265 groupMenu.add(unGroupMenuItem);
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266 groupMenu.add(colourMenu);
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267 groupMenu.addSeparator();
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268 groupMenu.add(showBoxes);
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269 groupMenu.add(showText);
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270 groupMenu.add(showColourText);
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271 groupMenu.addSeparator();
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272 groupMenu.add(outline);
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273 sequenceMenu.add(sequenceName);
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274 sequenceMenu.add(pdbMenuItem);
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275 colourMenu.add(noColourmenuItem);
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276 colourMenu.add(clustalColour);
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277 colourMenu.add(BLOSUM62Colour);
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278 colourMenu.add(PIDColour);
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279 colourMenu.add(zappoColour);
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280 colourMenu.add(taylorColour);
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281 colourMenu.add(hydrophobicityColour);
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282 colourMenu.add(helixColour);
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283 colourMenu.add(strandColour);
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284 colourMenu.add(turnColour);
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285 colourMenu.add(buriedColour);
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286 colourMenu.add(nucleotideMenuItem);
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287 colourMenu.add(userDefinedColour);
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288 colourMenu.addSeparator();
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289 colourMenu.add(abovePIDColour);
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290 colourMenu.add(conservationMenuItem);
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291 noColourmenuItem.setText("None");
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292 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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294 public void actionPerformed(ActionEvent e)
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296 noColourmenuItem_actionPerformed(e);
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300 clustalColour.setText("Clustalx colours");
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301 clustalColour.addActionListener(new java.awt.event.ActionListener()
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303 public void actionPerformed(ActionEvent e)
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305 clustalColour_actionPerformed(e);
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308 zappoColour.setText("Zappo");
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309 zappoColour.addActionListener(new java.awt.event.ActionListener()
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311 public void actionPerformed(ActionEvent e)
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313 zappoColour_actionPerformed(e);
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316 taylorColour.setText("Taylor");
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317 taylorColour.addActionListener(new java.awt.event.ActionListener()
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319 public void actionPerformed(ActionEvent e)
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321 taylorColour_actionPerformed(e);
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324 hydrophobicityColour.setText("Hydrophobicity");
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325 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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327 public void actionPerformed(ActionEvent e)
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329 hydrophobicityColour_actionPerformed(e);
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332 helixColour.setText("Helix propensity");
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333 helixColour.addActionListener(new java.awt.event.ActionListener()
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335 public void actionPerformed(ActionEvent e)
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337 helixColour_actionPerformed(e);
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340 strandColour.setText("Strand propensity");
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341 strandColour.addActionListener(new java.awt.event.ActionListener()
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343 public void actionPerformed(ActionEvent e)
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345 strandColour_actionPerformed(e);
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348 turnColour.setText("Turn propensity");
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349 turnColour.addActionListener(new java.awt.event.ActionListener()
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351 public void actionPerformed(ActionEvent e)
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353 turnColour_actionPerformed(e);
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356 buriedColour.setText("Buried Index");
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357 buriedColour.addActionListener(new java.awt.event.ActionListener()
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359 public void actionPerformed(ActionEvent e)
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361 buriedColour_actionPerformed(e);
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364 abovePIDColour.setText("Above % Identity");
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365 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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367 public void actionPerformed(ActionEvent e)
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369 abovePIDColour_actionPerformed(e);
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372 userDefinedColour.setText("User Defined");
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373 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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375 public void actionPerformed(ActionEvent e)
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377 userDefinedColour_actionPerformed(e);
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380 PIDColour.setText("Percentage Identity");
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381 PIDColour.addActionListener(new java.awt.event.ActionListener()
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383 public void actionPerformed(ActionEvent e)
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385 PIDColour_actionPerformed(e);
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388 BLOSUM62Colour.setText("BLOSUM62");
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389 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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391 public void actionPerformed(ActionEvent e)
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393 BLOSUM62Colour_actionPerformed(e);
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396 conservationMenuItem.setText("Conservation");
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397 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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399 public void actionPerformed(ActionEvent e)
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401 conservationMenuItem_actionPerformed(e);
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408 SequenceGroup sg = getGroup();
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409 SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
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411 if (superG != null)
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413 superG.setSuperGroupProperties(sg);
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416 ap.seqPanel.repaint();
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419 protected void clustalColour_actionPerformed(ActionEvent e)
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421 SequenceGroup sg = getGroup();
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422 sg.cs = new ClustalxColourScheme(sg.sequences,
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423 ap.av.alignment.getWidth());
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427 protected void zappoColour_actionPerformed(ActionEvent e)
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429 getGroup().cs = new ZappoColourScheme();
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433 protected void taylorColour_actionPerformed(ActionEvent e)
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435 getGroup().cs = new TaylorColourScheme();
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439 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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441 getGroup().cs = new HydrophobicColourScheme();
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445 protected void helixColour_actionPerformed(ActionEvent e)
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447 getGroup().cs = new HelixColourScheme();
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451 protected void strandColour_actionPerformed(ActionEvent e)
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453 getGroup().cs = new StrandColourScheme();
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457 protected void turnColour_actionPerformed(ActionEvent e)
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459 getGroup().cs = new TurnColourScheme();
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463 protected void buriedColour_actionPerformed(ActionEvent e)
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465 getGroup().cs = new BuriedColourScheme();
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469 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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471 getGroup().cs = new NucleotideColourScheme();
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475 protected void abovePIDColour_actionPerformed(ActionEvent e)
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477 SequenceGroup sg = getGroup();
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479 if (abovePIDColour.isSelected())
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481 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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482 ap.av.alignment.getWidth()));
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484 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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485 getGroup().getName());
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487 if (sg.cs instanceof ResidueColourScheme)
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489 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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491 else if (sg.cs instanceof ScoreColourScheme)
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493 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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496 SliderPanel.showPIDSlider();
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498 else // remove PIDColouring
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500 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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501 rcs.setThreshold(0);
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508 protected void userDefinedColour_actionPerformed(ActionEvent e)
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510 new UserDefinedColours(ap, getGroup());
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513 protected void PIDColour_actionPerformed(ActionEvent e)
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515 SequenceGroup sg = getGroup();
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516 sg.cs = new PIDColourScheme();
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517 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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518 ap.av.alignment.getWidth()));
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522 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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524 SequenceGroup sg = getGroup();
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526 sg.cs = new Blosum62ColourScheme();
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528 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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529 ap.av.alignment.getWidth()));
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534 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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536 getGroup().cs = null;
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540 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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542 SequenceGroup sg = getGroup();
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544 if (conservationMenuItem.isSelected())
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546 Conservation c = new Conservation("Group",
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547 ResidueProperties.propHash, 3,
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549 ap.av.alignment.getWidth());
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552 c.verdict(false, ap.av.ConsPercGaps);
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554 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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558 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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559 SliderPanel.showConservationSlider();
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561 else // remove ConservationColouring
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563 ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
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570 protected void groupName_actionPerformed(ActionEvent e)
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572 SequenceGroup sg = getGroup();
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573 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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574 "Enter new group name", "Edit group name",
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575 JOptionPane.QUESTION_MESSAGE);
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583 groupName.setText(reply);
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586 protected void analyze_actionPerformed(ActionEvent e)
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588 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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589 JInternalFrame frame = new JInternalFrame();
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590 frame.setContentPane(cap);
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591 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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593 SequenceGroup sg = getGroup();
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594 StringBuffer sb = new StringBuffer();
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596 for (int i = 0; i < sg.sequences.size(); i++)
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598 Sequence tmp = (Sequence) sg.sequences.get(i);
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599 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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603 sb.append("Something amazing will happen soon");
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604 cap.setText(sb.toString());
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607 SequenceGroup getGroup()
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609 SequenceGroup sg = ap.av.getSelectionGroup();
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611 // this method won't add a new group if it already exists
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612 ap.av.alignment.addGroup(sg);
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617 void sequenceName_actionPerformed(ActionEvent e)
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619 String id = sequence.getName();
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620 String s = (String) JOptionPane.showInternalInputDialog(ap,
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621 "Edit sequence name",
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622 "Edit sequence name (" + sequence.getName() + ")",
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623 JOptionPane.PLAIN_MESSAGE, null, null, id);
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627 sequence.setName(s);
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632 void unGroupMenuItem_actionPerformed(ActionEvent e)
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634 SequenceGroup sg = ap.av.getSelectionGroup();
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635 ap.av.alignment.deleteGroup(sg);
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636 ap.av.setSelectionGroup(null);
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640 void pdbMenuItem_actionPerformed(ActionEvent e)
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642 if (sequence.getPDBId() == null)
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649 EBIFetchClient ebi = new EBIFetchClient();
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650 String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
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653 PDBfile pdb = new PDBfile(result);
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655 rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
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656 JInternalFrame frame = new JInternalFrame();
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657 frame.setContentPane(rc);
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658 Desktop.addInternalFrame(frame,
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659 sequence.getName() + " " + sequence.getPDBId(),
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662 catch (Exception ex)
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664 ex.printStackTrace();
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668 protected void outline_actionPerformed(ActionEvent e)
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670 SequenceGroup sg = getGroup();
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671 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
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676 sg.setOutlineColour(col);
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682 public void showBoxes_actionPerformed(ActionEvent e)
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684 getGroup().setDisplayBoxes(showBoxes.isSelected());
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688 public void showText_actionPerformed(ActionEvent e)
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690 getGroup().setDisplayText(showText.isSelected());
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694 public void showColourText_actionPerformed(ActionEvent e)
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696 getGroup().setColourText(showColourText.isSelected());
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