3 import jalview.datamodel.*;
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4 import jalview.analysis.*;
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5 import jalview.schemes.*;
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7 import javax.swing.*;
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8 import java.awt.event.*;
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12 public class PopupMenu extends JPopupMenu
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14 JMenu groupMenu = new JMenu();
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15 JMenuItem groupName = new JMenuItem();
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16 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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17 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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18 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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19 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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20 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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21 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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22 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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23 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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24 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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25 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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26 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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27 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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28 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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29 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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33 JMenu sequenceMenu = new JMenu();
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34 JMenuItem sequenceName = new JMenuItem();
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36 JMenuItem unGroupMenuItem = new JMenuItem();
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37 JMenuItem pdbMenuItem = new JMenuItem();
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38 JMenuItem outline = new JMenuItem();
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39 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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40 JMenu colourMenu = new JMenu();
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41 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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42 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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43 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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45 public PopupMenu(AlignmentPanel ap, Sequence seq)
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47 ///////////////////////////////////////////////////////////
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48 // If this is activated from the sequence panel, the user may want to
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49 // edit or annotate a particular residue. Therefore display the residue menu
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51 // If from the IDPanel, we must display the sequence menu
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52 //////////////////////////////////////////////////////////
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57 ButtonGroup colours = new ButtonGroup();
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58 colours.add(noColourmenuItem);
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59 colours.add(clustalColour);
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60 colours.add(zappoColour);
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61 colours.add(taylorColour);
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62 colours.add(hydrophobicityColour);
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63 colours.add(helixColour);
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64 colours.add(strandColour);
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65 colours.add(turnColour);
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66 colours.add(buriedColour);
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67 colours.add(abovePIDColour);
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68 colours.add(userDefinedColour);
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69 colours.add(PIDColour);
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70 colours.add(BLOSUM62Colour);
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75 { e.printStackTrace(); }
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77 SequenceGroup sg = ap.av.getSelectionGroup();
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80 groupName.setText(sg.getName());
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81 if(sg.cs instanceof ZappoColourScheme)
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82 zappoColour.setSelected(true);
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83 else if(sg.cs instanceof TaylorColourScheme)
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84 taylorColour.setSelected(true);
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85 else if (sg.cs instanceof PIDColourScheme)
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86 PIDColour.setSelected(true);
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87 else if (sg.cs instanceof Blosum62ColourScheme)
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88 BLOSUM62Colour.setSelected(true);
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89 else if (sg.cs instanceof UserColourScheme)
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90 userDefinedColour.setSelected(true);
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91 else if (sg.cs instanceof HydrophobicColourScheme)
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92 hydrophobicityColour.setSelected(true);
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93 else if (sg.cs instanceof HelixColourScheme)
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94 helixColour.setSelected(true);
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95 else if (sg.cs instanceof StrandColourScheme)
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96 strandColour.setSelected(true);
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97 else if (sg.cs instanceof TurnColourScheme)
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98 turnColour.setSelected(true);
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99 else if (sg.cs instanceof BuriedColourScheme)
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100 buriedColour.setSelected(true);
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101 else if (sg.cs instanceof ClustalxColourScheme)
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102 clustalColour.setSelected(true);
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104 noColourmenuItem.setSelected(true);
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106 if (sg.cs instanceof ConservationColourScheme)
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107 conservationMenuItem.setSelected(true);
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109 showText.setSelected(sg.getDisplayText());
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110 showColourText.setSelected(sg.getColourText());
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111 showBoxes.setSelected(sg.getDisplayBoxes());
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114 if( !ap.av.alignment.getGroups().contains(sg))
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115 unGroupMenuItem.setVisible(false);
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117 groupMenu.insertSeparator(3);
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120 sequenceMenu.setVisible(false);
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123 private void jbInit() throws Exception
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125 groupMenu.setText("Group");
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126 groupMenu.setText("Define");
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127 groupName.setText("Name");
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128 groupName.addActionListener(new java.awt.event.ActionListener()
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130 public void actionPerformed(ActionEvent e)
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132 groupName_actionPerformed(e);
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135 sequenceMenu.setText("Sequence");
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136 sequenceName.setText("Edit name");
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137 sequenceName.addActionListener(new java.awt.event.ActionListener()
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139 public void actionPerformed(ActionEvent e)
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141 sequenceName_actionPerformed(e);
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144 PIDColour.setFocusPainted(false);
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145 unGroupMenuItem.setText("Remove Group");
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146 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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148 public void actionPerformed(ActionEvent e)
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150 unGroupMenuItem_actionPerformed(e);
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153 pdbMenuItem.setText("View PDB structure");
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154 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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156 public void actionPerformed(ActionEvent e)
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158 pdbMenuItem_actionPerformed(e);
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161 outline.setText("Border colour");
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162 outline.addActionListener(new java.awt.event.ActionListener()
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164 public void actionPerformed(ActionEvent e)
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166 outline_actionPerformed(e);
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169 nucleotideMenuItem.setText("Nucleotide");
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170 nucleotideMenuItem.addActionListener(new ActionListener()
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172 public void actionPerformed(ActionEvent e)
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174 nucleotideMenuItem_actionPerformed(e);
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177 colourMenu.setText("Group Colour");
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178 showBoxes.setText("Boxes");
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179 showBoxes.setState(true);
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180 showBoxes.addActionListener(new ActionListener()
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182 public void actionPerformed(ActionEvent e)
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184 showBoxes_actionPerformed(e);
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187 showText.setText("Text");
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188 showText.setState(true);
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189 showText.addActionListener(new ActionListener()
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191 public void actionPerformed(ActionEvent e)
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193 showText_actionPerformed(e);
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196 showColourText.setText("Colour Text");
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197 showColourText.addActionListener(new ActionListener()
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199 public void actionPerformed(ActionEvent e)
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201 showColourText_actionPerformed(e);
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206 groupMenu.add(groupName);
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207 groupMenu.addSeparator();
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208 groupMenu.add(unGroupMenuItem);
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209 groupMenu.add(colourMenu);
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210 groupMenu.addSeparator();
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211 groupMenu.add(showBoxes);
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212 groupMenu.add(showText);
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213 groupMenu.add(showColourText);
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214 groupMenu.addSeparator();
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215 groupMenu.add(outline);
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216 sequenceMenu.add(sequenceName);
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217 sequenceMenu.add(pdbMenuItem);
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218 colourMenu.add(noColourmenuItem);
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219 colourMenu.add(clustalColour);
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220 colourMenu.add(BLOSUM62Colour);
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221 colourMenu.add(PIDColour);
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222 colourMenu.add(zappoColour);
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223 colourMenu.add(taylorColour);
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224 colourMenu.add(hydrophobicityColour);
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225 colourMenu.add(helixColour);
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226 colourMenu.add(strandColour);
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227 colourMenu.add(turnColour);
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228 colourMenu.add(buriedColour);
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229 colourMenu.add(nucleotideMenuItem);
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230 colourMenu.add(userDefinedColour);
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231 colourMenu.addSeparator();
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232 colourMenu.add(abovePIDColour);
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233 colourMenu.add(conservationMenuItem);
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234 noColourmenuItem.setText("None");
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235 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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237 public void actionPerformed(ActionEvent e)
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239 noColourmenuItem_actionPerformed(e);
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243 clustalColour.setText("Clustalx colours");
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244 clustalColour.addActionListener(new java.awt.event.ActionListener()
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246 public void actionPerformed(ActionEvent e)
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248 clustalColour_actionPerformed(e);
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251 zappoColour.setText("Zappo");
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252 zappoColour.addActionListener(new java.awt.event.ActionListener()
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254 public void actionPerformed(ActionEvent e)
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256 zappoColour_actionPerformed(e);
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259 taylorColour.setText("Taylor");
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260 taylorColour.addActionListener(new java.awt.event.ActionListener()
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262 public void actionPerformed(ActionEvent e)
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264 taylorColour_actionPerformed(e);
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267 hydrophobicityColour.setText("Hydrophobicity");
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268 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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270 public void actionPerformed(ActionEvent e)
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272 hydrophobicityColour_actionPerformed(e);
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275 helixColour.setText("Helix propensity");
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276 helixColour.addActionListener(new java.awt.event.ActionListener()
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278 public void actionPerformed(ActionEvent e)
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280 helixColour_actionPerformed(e);
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283 strandColour.setText("Strand propensity");
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284 strandColour.addActionListener(new java.awt.event.ActionListener()
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286 public void actionPerformed(ActionEvent e)
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288 strandColour_actionPerformed(e);
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291 turnColour.setText("Turn propensity");
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292 turnColour.addActionListener(new java.awt.event.ActionListener()
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294 public void actionPerformed(ActionEvent e)
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296 turnColour_actionPerformed(e);
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299 buriedColour.setText("Buried Index");
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300 buriedColour.addActionListener(new java.awt.event.ActionListener()
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302 public void actionPerformed(ActionEvent e)
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304 buriedColour_actionPerformed(e);
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307 abovePIDColour.setText("Above % Identity");
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308 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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310 public void actionPerformed(ActionEvent e)
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312 abovePIDColour_actionPerformed(e);
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315 userDefinedColour.setText("User Defined");
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316 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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318 public void actionPerformed(ActionEvent e)
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320 userDefinedColour_actionPerformed(e);
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323 PIDColour.setText("Percentage Identity");
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324 PIDColour.addActionListener(new java.awt.event.ActionListener()
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326 public void actionPerformed(ActionEvent e)
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328 PIDColour_actionPerformed(e);
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331 BLOSUM62Colour.setText("BLOSUM62");
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332 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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334 public void actionPerformed(ActionEvent e)
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336 BLOSUM62Colour_actionPerformed(e);
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339 conservationMenuItem.setText("Conservation");
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340 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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342 public void actionPerformed(ActionEvent e)
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344 conservationMenuItem_actionPerformed(e);
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354 SequenceGroup sg = getGroup();
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355 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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357 superG.setSuperGroupProperties( sg );
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359 ap.seqPanel.repaint();
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362 protected void clustalColour_actionPerformed(ActionEvent e)
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364 SequenceGroup sg = getGroup();
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365 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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369 protected void zappoColour_actionPerformed(ActionEvent e)
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371 getGroup().cs = new ZappoColourScheme();
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375 protected void taylorColour_actionPerformed(ActionEvent e)
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377 getGroup().cs = new TaylorColourScheme();
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382 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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384 getGroup().cs = new HydrophobicColourScheme();
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388 protected void helixColour_actionPerformed(ActionEvent e)
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390 getGroup().cs = new HelixColourScheme();
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394 protected void strandColour_actionPerformed(ActionEvent e)
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396 getGroup().cs = new StrandColourScheme();
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400 protected void turnColour_actionPerformed(ActionEvent e)
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402 getGroup().cs = new TurnColourScheme();
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406 protected void buriedColour_actionPerformed(ActionEvent e)
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408 getGroup().cs = new BuriedColourScheme();
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412 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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414 getGroup().cs = new NucleotideColourScheme();
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420 protected void abovePIDColour_actionPerformed(ActionEvent e)
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422 SequenceGroup sg = getGroup();
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423 if (abovePIDColour.isSelected())
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425 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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426 ap.av.alignment.getWidth()));
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427 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
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428 if (sg.cs instanceof ResidueColourScheme)
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429 ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
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430 else if (sg.cs instanceof ScoreColourScheme)
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431 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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433 SliderPanel.showPIDSlider();
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437 else // remove PIDColouring
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439 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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440 rcs.setThreshold(0);
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449 protected void userDefinedColour_actionPerformed(ActionEvent e)
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451 new UserDefinedColours( ap, getGroup());
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454 protected void PIDColour_actionPerformed(ActionEvent e)
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456 SequenceGroup sg = getGroup();
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457 sg.cs = new PIDColourScheme();
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458 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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459 ap.av.alignment.getWidth()));
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463 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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465 SequenceGroup sg = getGroup();
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467 sg.cs = new Blosum62ColourScheme();
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469 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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470 ap.av.alignment.getWidth()));
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476 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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478 getGroup().cs = null;
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482 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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484 SequenceGroup sg = getGroup();
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486 if(conservationMenuItem.isSelected())
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489 Conservation c = new Conservation("Group",
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490 ResidueProperties.propHash, 3,
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492 ap.av.alignment.getWidth());
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495 c.verdict(false, ap.av.ConsPercGaps);
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496 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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501 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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502 SliderPanel.showConservationSlider();
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504 else // remove ConservationColouring
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506 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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514 protected void groupName_actionPerformed(ActionEvent e)
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516 SequenceGroup sg = getGroup();
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517 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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522 groupName.setText(reply);
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526 protected void analyze_actionPerformed(ActionEvent e)
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528 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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529 JInternalFrame frame = new JInternalFrame();
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530 frame.setContentPane(cap);
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531 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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532 SequenceGroup sg = getGroup();
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533 StringBuffer sb = new StringBuffer();
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535 for(int i=0; i<sg.sequences.size(); i++)
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537 Sequence tmp = (Sequence)sg.sequences.get(i);
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538 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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542 sb.append("Something amazing will happen soon");
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543 cap.setText( sb.toString() );
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547 SequenceGroup getGroup()
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549 SequenceGroup sg = ap.av.getSelectionGroup();
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551 // this method won't add a new group if it already exists
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552 ap.av.alignment.addGroup(sg);
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557 void sequenceName_actionPerformed(ActionEvent e)
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559 String id = sequence.getName();
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560 String s = (String)JOptionPane.showInternalInputDialog(
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562 "Edit sequence name",
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563 "Edit sequence name ("+sequence.getName()+")",
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564 JOptionPane.PLAIN_MESSAGE,
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571 sequence.setName(s);
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577 void unGroupMenuItem_actionPerformed(ActionEvent e)
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579 SequenceGroup sg = ap.av.getSelectionGroup();
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580 ap.av.alignment.deleteGroup(sg);
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581 ap.av.setSelectionGroup(null);
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585 void pdbMenuItem_actionPerformed(ActionEvent e)
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587 if(sequence.getPDBId()==null)
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592 EBIFetchClient ebi = new EBIFetchClient();
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593 String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
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595 PDBfile pdb = new PDBfile(result);
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597 rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
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598 JInternalFrame frame = new JInternalFrame();
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599 frame.setContentPane(rc);
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600 Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
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602 catch (Exception ex)
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604 ex.printStackTrace();
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608 protected void outline_actionPerformed(ActionEvent e)
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610 SequenceGroup sg = getGroup();
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611 Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
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613 sg.setOutlineColour(col);
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617 public void showBoxes_actionPerformed(ActionEvent e)
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619 getGroup().setDisplayBoxes(showBoxes.isSelected());
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623 public void showText_actionPerformed(ActionEvent e)
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625 getGroup().setDisplayText(showText.isSelected());
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629 public void showColourText_actionPerformed(ActionEvent e)
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631 getGroup().setColourText(showColourText.isSelected());
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