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 if(seq.getPDBId()==null)
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100 pdbMenuItem.setVisible(false);
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102 SequenceGroup sg = ap.av.getSelectionGroup();
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106 groupName.setText(sg.getName());
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108 if (sg.cs instanceof ZappoColourScheme)
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110 zappoColour.setSelected(true);
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112 else if (sg.cs instanceof TaylorColourScheme)
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114 taylorColour.setSelected(true);
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116 else if (sg.cs instanceof PIDColourScheme)
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118 PIDColour.setSelected(true);
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120 else if (sg.cs instanceof Blosum62ColourScheme)
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122 BLOSUM62Colour.setSelected(true);
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124 else if (sg.cs instanceof UserColourScheme)
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126 userDefinedColour.setSelected(true);
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128 else if (sg.cs instanceof HydrophobicColourScheme)
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130 hydrophobicityColour.setSelected(true);
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132 else if (sg.cs instanceof HelixColourScheme)
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134 helixColour.setSelected(true);
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136 else if (sg.cs instanceof StrandColourScheme)
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138 strandColour.setSelected(true);
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140 else if (sg.cs instanceof TurnColourScheme)
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142 turnColour.setSelected(true);
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144 else if (sg.cs instanceof BuriedColourScheme)
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146 buriedColour.setSelected(true);
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148 else if (sg.cs instanceof ClustalxColourScheme)
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150 clustalColour.setSelected(true);
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154 noColourmenuItem.setSelected(true);
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157 if (sg.cs instanceof ConservationColourScheme)
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159 conservationMenuItem.setSelected(true);
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162 showText.setSelected(sg.getDisplayText());
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163 showColourText.setSelected(sg.getColourText());
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164 showBoxes.setSelected(sg.getDisplayBoxes());
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167 if (!ap.av.alignment.getGroups().contains(sg))
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169 unGroupMenuItem.setVisible(false);
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173 groupMenu.insertSeparator(3);
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178 sequenceMenu.setVisible(false);
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182 private void jbInit()
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185 groupMenu.setText("Group");
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186 groupMenu.setText("Define");
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187 groupName.setText("Name");
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188 groupName.addActionListener(new java.awt.event.ActionListener()
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190 public void actionPerformed(ActionEvent e)
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192 groupName_actionPerformed(e);
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195 sequenceMenu.setText("Sequence");
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196 sequenceName.setText("Edit name");
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197 sequenceName.addActionListener(new java.awt.event.ActionListener()
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199 public void actionPerformed(ActionEvent e)
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201 sequenceName_actionPerformed(e);
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204 PIDColour.setFocusPainted(false);
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205 unGroupMenuItem.setText("Remove Group");
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206 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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208 public void actionPerformed(ActionEvent e)
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210 unGroupMenuItem_actionPerformed(e);
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213 pdbMenuItem.setText("View PDB structure");
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214 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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216 public void actionPerformed(ActionEvent e)
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218 pdbMenuItem_actionPerformed(e);
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221 outline.setText("Border colour");
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222 outline.addActionListener(new java.awt.event.ActionListener()
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224 public void actionPerformed(ActionEvent e)
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226 outline_actionPerformed(e);
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229 nucleotideMenuItem.setText("Nucleotide");
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230 nucleotideMenuItem.addActionListener(new ActionListener()
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232 public void actionPerformed(ActionEvent e)
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234 nucleotideMenuItem_actionPerformed(e);
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237 colourMenu.setText("Group Colour");
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238 showBoxes.setText("Boxes");
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239 showBoxes.setState(true);
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240 showBoxes.addActionListener(new ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 showBoxes_actionPerformed(e);
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247 showText.setText("Text");
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248 showText.setState(true);
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249 showText.addActionListener(new ActionListener()
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251 public void actionPerformed(ActionEvent e)
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253 showText_actionPerformed(e);
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256 showColourText.setText("Colour Text");
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257 showColourText.addActionListener(new ActionListener()
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259 public void actionPerformed(ActionEvent e)
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261 showColourText_actionPerformed(e);
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266 groupMenu.add(groupName);
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267 groupMenu.addSeparator();
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268 groupMenu.add(unGroupMenuItem);
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269 groupMenu.add(colourMenu);
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270 groupMenu.addSeparator();
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271 groupMenu.add(showBoxes);
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272 groupMenu.add(showText);
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273 groupMenu.add(showColourText);
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274 groupMenu.addSeparator();
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275 groupMenu.add(outline);
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276 sequenceMenu.add(sequenceName);
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277 sequenceMenu.add(pdbMenuItem);
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278 colourMenu.add(noColourmenuItem);
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279 colourMenu.add(clustalColour);
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280 colourMenu.add(BLOSUM62Colour);
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281 colourMenu.add(PIDColour);
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282 colourMenu.add(zappoColour);
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283 colourMenu.add(taylorColour);
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284 colourMenu.add(hydrophobicityColour);
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285 colourMenu.add(helixColour);
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286 colourMenu.add(strandColour);
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287 colourMenu.add(turnColour);
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288 colourMenu.add(buriedColour);
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289 colourMenu.add(nucleotideMenuItem);
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290 colourMenu.add(userDefinedColour);
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291 colourMenu.addSeparator();
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292 colourMenu.add(abovePIDColour);
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293 colourMenu.add(conservationMenuItem);
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294 noColourmenuItem.setText("None");
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295 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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297 public void actionPerformed(ActionEvent e)
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299 noColourmenuItem_actionPerformed(e);
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303 clustalColour.setText("Clustalx colours");
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304 clustalColour.addActionListener(new java.awt.event.ActionListener()
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306 public void actionPerformed(ActionEvent e)
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308 clustalColour_actionPerformed(e);
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311 zappoColour.setText("Zappo");
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312 zappoColour.addActionListener(new java.awt.event.ActionListener()
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314 public void actionPerformed(ActionEvent e)
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316 zappoColour_actionPerformed(e);
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319 taylorColour.setText("Taylor");
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320 taylorColour.addActionListener(new java.awt.event.ActionListener()
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322 public void actionPerformed(ActionEvent e)
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324 taylorColour_actionPerformed(e);
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327 hydrophobicityColour.setText("Hydrophobicity");
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328 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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330 public void actionPerformed(ActionEvent e)
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332 hydrophobicityColour_actionPerformed(e);
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335 helixColour.setText("Helix propensity");
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336 helixColour.addActionListener(new java.awt.event.ActionListener()
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338 public void actionPerformed(ActionEvent e)
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340 helixColour_actionPerformed(e);
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343 strandColour.setText("Strand propensity");
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344 strandColour.addActionListener(new java.awt.event.ActionListener()
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346 public void actionPerformed(ActionEvent e)
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348 strandColour_actionPerformed(e);
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351 turnColour.setText("Turn propensity");
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352 turnColour.addActionListener(new java.awt.event.ActionListener()
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354 public void actionPerformed(ActionEvent e)
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356 turnColour_actionPerformed(e);
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359 buriedColour.setText("Buried Index");
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360 buriedColour.addActionListener(new java.awt.event.ActionListener()
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362 public void actionPerformed(ActionEvent e)
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364 buriedColour_actionPerformed(e);
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367 abovePIDColour.setText("Above % Identity");
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368 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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370 public void actionPerformed(ActionEvent e)
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372 abovePIDColour_actionPerformed(e);
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375 userDefinedColour.setText("User Defined");
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376 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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378 public void actionPerformed(ActionEvent e)
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380 userDefinedColour_actionPerformed(e);
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383 PIDColour.setText("Percentage Identity");
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384 PIDColour.addActionListener(new java.awt.event.ActionListener()
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386 public void actionPerformed(ActionEvent e)
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388 PIDColour_actionPerformed(e);
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391 BLOSUM62Colour.setText("BLOSUM62");
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392 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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394 public void actionPerformed(ActionEvent e)
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396 BLOSUM62Colour_actionPerformed(e);
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399 conservationMenuItem.setText("Conservation");
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400 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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402 public void actionPerformed(ActionEvent e)
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404 conservationMenuItem_actionPerformed(e);
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411 SequenceGroup sg = getGroup();
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412 SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
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414 if (superG != null)
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416 superG.setSuperGroupProperties(sg);
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419 ap.seqPanel.repaint();
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422 protected void clustalColour_actionPerformed(ActionEvent e)
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424 SequenceGroup sg = getGroup();
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425 sg.cs = new ClustalxColourScheme(sg.sequences,
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426 ap.av.alignment.getWidth());
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430 protected void zappoColour_actionPerformed(ActionEvent e)
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432 getGroup().cs = new ZappoColourScheme();
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436 protected void taylorColour_actionPerformed(ActionEvent e)
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438 getGroup().cs = new TaylorColourScheme();
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442 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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444 getGroup().cs = new HydrophobicColourScheme();
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448 protected void helixColour_actionPerformed(ActionEvent e)
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450 getGroup().cs = new HelixColourScheme();
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454 protected void strandColour_actionPerformed(ActionEvent e)
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456 getGroup().cs = new StrandColourScheme();
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460 protected void turnColour_actionPerformed(ActionEvent e)
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462 getGroup().cs = new TurnColourScheme();
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466 protected void buriedColour_actionPerformed(ActionEvent e)
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468 getGroup().cs = new BuriedColourScheme();
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472 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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474 getGroup().cs = new NucleotideColourScheme();
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478 protected void abovePIDColour_actionPerformed(ActionEvent e)
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480 SequenceGroup sg = getGroup();
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482 if (abovePIDColour.isSelected())
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484 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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485 ap.av.alignment.getWidth()));
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487 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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488 getGroup().getName());
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490 if (sg.cs instanceof ResidueColourScheme)
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492 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
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494 else if (sg.cs instanceof ScoreColourScheme)
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496 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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499 SliderPanel.showPIDSlider();
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501 else // remove PIDColouring
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503 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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504 rcs.setThreshold(0);
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511 protected void userDefinedColour_actionPerformed(ActionEvent e)
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513 new UserDefinedColours(ap, getGroup());
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516 protected void PIDColour_actionPerformed(ActionEvent e)
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518 SequenceGroup sg = getGroup();
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519 sg.cs = new PIDColourScheme();
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520 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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521 ap.av.alignment.getWidth()));
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525 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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527 SequenceGroup sg = getGroup();
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529 sg.cs = new Blosum62ColourScheme();
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531 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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532 ap.av.alignment.getWidth()));
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537 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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539 getGroup().cs = null;
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543 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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545 SequenceGroup sg = getGroup();
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547 if (conservationMenuItem.isSelected())
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549 Conservation c = new Conservation("Group",
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550 ResidueProperties.propHash, 3,
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552 ap.av.alignment.getWidth());
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555 c.verdict(false, ap.av.ConsPercGaps);
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557 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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561 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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562 SliderPanel.showConservationSlider();
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564 else // remove ConservationColouring
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566 ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
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573 protected void groupName_actionPerformed(ActionEvent e)
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575 SequenceGroup sg = getGroup();
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576 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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577 "Enter new group name", "Edit group name",
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578 JOptionPane.QUESTION_MESSAGE);
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586 groupName.setText(reply);
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589 protected void analyze_actionPerformed(ActionEvent e)
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591 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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592 JInternalFrame frame = new JInternalFrame();
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593 frame.setContentPane(cap);
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594 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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596 SequenceGroup sg = getGroup();
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597 StringBuffer sb = new StringBuffer();
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599 for (int i = 0; i < sg.sequences.size(); i++)
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601 Sequence tmp = (Sequence) sg.sequences.get(i);
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602 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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606 sb.append("Something amazing will happen soon");
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607 cap.setText(sb.toString());
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610 SequenceGroup getGroup()
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612 SequenceGroup sg = ap.av.getSelectionGroup();
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614 // this method won't add a new group if it already exists
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615 ap.av.alignment.addGroup(sg);
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620 void sequenceName_actionPerformed(ActionEvent e)
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622 String id = sequence.getName();
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623 String s = (String) JOptionPane.showInternalInputDialog(ap,
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624 "Edit sequence name",
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625 "Edit sequence name (" + sequence.getName() + ")",
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626 JOptionPane.PLAIN_MESSAGE, null, null, id);
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630 if(s.indexOf(" ")>-1)
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631 JOptionPane.showMessageDialog(ap, "Spaces have been converted to \"_\"",
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632 "No spaces allowed in Sequence Name", JOptionPane.WARNING_MESSAGE);
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633 s = s.replace(' ', '_');
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634 sequence.setName(s);
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639 void unGroupMenuItem_actionPerformed(ActionEvent e)
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641 SequenceGroup sg = ap.av.getSelectionGroup();
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642 ap.av.alignment.deleteGroup(sg);
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643 ap.av.setSelectionGroup(null);
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647 void pdbMenuItem_actionPerformed(ActionEvent e)
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649 if (sequence.getPDBId() == null)
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656 EBIFetchClient ebi = new EBIFetchClient();
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657 String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,
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660 PDBfile pdb = new PDBfile(result);
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662 rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
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663 JInternalFrame frame = new JInternalFrame();
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664 frame.setContentPane(rc);
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665 Desktop.addInternalFrame(frame,
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666 sequence.getName() + " " + sequence.getPDBId(),
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669 catch (Exception ex)
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671 ex.printStackTrace();
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675 protected void outline_actionPerformed(ActionEvent e)
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677 SequenceGroup sg = getGroup();
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678 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
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683 sg.setOutlineColour(col);
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689 public void showBoxes_actionPerformed(ActionEvent e)
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691 getGroup().setDisplayBoxes(showBoxes.isSelected());
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695 public void showText_actionPerformed(ActionEvent e)
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697 getGroup().setDisplayText(showText.isSelected());
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701 public void showColourText_actionPerformed(ActionEvent e)
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703 getGroup().setColourText(showColourText.isSelected());
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