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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118 sequenceMenu.setVisible(false);
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121 private void jbInit() throws Exception
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123 groupMenu.setText("Group");
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124 groupMenu.setText("Define");
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125 groupName.setText("Name");
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126 groupName.addActionListener(new java.awt.event.ActionListener()
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128 public void actionPerformed(ActionEvent e)
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130 groupName_actionPerformed(e);
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133 sequenceMenu.setText("Sequence");
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134 sequenceName.setText("Edit name");
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135 sequenceName.addActionListener(new java.awt.event.ActionListener()
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137 public void actionPerformed(ActionEvent e)
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139 sequenceName_actionPerformed(e);
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142 PIDColour.setFocusPainted(false);
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143 unGroupMenuItem.setText("Remove Group");
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144 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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146 public void actionPerformed(ActionEvent e)
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148 unGroupMenuItem_actionPerformed(e);
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151 pdbMenuItem.setText("View PDB structure");
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152 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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154 public void actionPerformed(ActionEvent e)
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156 pdbMenuItem_actionPerformed(e);
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159 outline.setText("Border colour");
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160 outline.addActionListener(new java.awt.event.ActionListener()
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162 public void actionPerformed(ActionEvent e)
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164 outline_actionPerformed(e);
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167 nucleotideMenuItem.setText("Nucleotide");
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168 nucleotideMenuItem.addActionListener(new ActionListener()
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170 public void actionPerformed(ActionEvent e)
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172 nucleotideMenuItem_actionPerformed(e);
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175 colourMenu.setText("Group Colour");
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176 showBoxes.setText("Boxes");
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177 showBoxes.setState(true);
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178 showBoxes.addActionListener(new ActionListener()
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180 public void actionPerformed(ActionEvent e)
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182 showBoxes_actionPerformed(e);
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185 showText.setText("Text");
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186 showText.setState(true);
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187 showText.addActionListener(new ActionListener()
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189 public void actionPerformed(ActionEvent e)
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191 showText_actionPerformed(e);
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194 showColourText.setText("Colour Text");
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195 showColourText.addActionListener(new ActionListener()
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197 public void actionPerformed(ActionEvent e)
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199 showColourText_actionPerformed(e);
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204 groupMenu.add(groupName);
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205 groupMenu.addSeparator();
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206 groupMenu.add(unGroupMenuItem);
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207 groupMenu.addSeparator();
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208 groupMenu.add(colourMenu);
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209 groupMenu.addSeparator();
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210 groupMenu.add(showBoxes);
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211 groupMenu.add(showText);
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212 groupMenu.add(showColourText);
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213 groupMenu.addSeparator();
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214 groupMenu.add(outline);
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215 sequenceMenu.add(sequenceName);
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216 sequenceMenu.add(pdbMenuItem);
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217 colourMenu.add(noColourmenuItem);
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218 colourMenu.add(clustalColour);
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219 colourMenu.add(BLOSUM62Colour);
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220 colourMenu.add(PIDColour);
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221 colourMenu.add(zappoColour);
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222 colourMenu.add(taylorColour);
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223 colourMenu.add(hydrophobicityColour);
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224 colourMenu.add(helixColour);
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225 colourMenu.add(strandColour);
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226 colourMenu.add(turnColour);
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227 colourMenu.add(buriedColour);
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228 colourMenu.add(nucleotideMenuItem);
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229 colourMenu.add(userDefinedColour);
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230 colourMenu.addSeparator();
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231 colourMenu.add(abovePIDColour);
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232 colourMenu.add(conservationMenuItem);
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233 noColourmenuItem.setText("None");
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234 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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236 public void actionPerformed(ActionEvent e)
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238 noColourmenuItem_actionPerformed(e);
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242 clustalColour.setText("Clustalx colours");
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243 clustalColour.addActionListener(new java.awt.event.ActionListener()
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245 public void actionPerformed(ActionEvent e)
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247 clustalColour_actionPerformed(e);
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250 zappoColour.setText("Zappo");
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251 zappoColour.addActionListener(new java.awt.event.ActionListener()
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253 public void actionPerformed(ActionEvent e)
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255 zappoColour_actionPerformed(e);
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258 taylorColour.setText("Taylor");
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259 taylorColour.addActionListener(new java.awt.event.ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 taylorColour_actionPerformed(e);
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266 hydrophobicityColour.setText("Hydrophobicity");
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267 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 hydrophobicityColour_actionPerformed(e);
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274 helixColour.setText("Helix propensity");
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275 helixColour.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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279 helixColour_actionPerformed(e);
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282 strandColour.setText("Strand propensity");
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283 strandColour.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 strandColour_actionPerformed(e);
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290 turnColour.setText("Turn propensity");
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291 turnColour.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 turnColour_actionPerformed(e);
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298 buriedColour.setText("Buried Index");
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299 buriedColour.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 buriedColour_actionPerformed(e);
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306 abovePIDColour.setText("Above % Identity");
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307 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 abovePIDColour_actionPerformed(e);
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314 userDefinedColour.setText("User Defined");
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315 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 userDefinedColour_actionPerformed(e);
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322 PIDColour.setText("Percentage Identity");
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323 PIDColour.addActionListener(new java.awt.event.ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 PIDColour_actionPerformed(e);
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330 BLOSUM62Colour.setText("BLOSUM62");
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331 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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333 public void actionPerformed(ActionEvent e)
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335 BLOSUM62Colour_actionPerformed(e);
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338 conservationMenuItem.setText("Conservation");
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339 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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341 public void actionPerformed(ActionEvent e)
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343 conservationMenuItem_actionPerformed(e);
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353 SequenceGroup sg = getGroup();
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354 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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356 superG.setSuperGroupProperties( sg );
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358 ap.seqPanel.repaint();
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361 protected void clustalColour_actionPerformed(ActionEvent e)
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363 SequenceGroup sg = getGroup();
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364 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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368 protected void zappoColour_actionPerformed(ActionEvent e)
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370 getGroup().cs = new ZappoColourScheme();
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374 protected void taylorColour_actionPerformed(ActionEvent e)
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376 getGroup().cs = new TaylorColourScheme();
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381 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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383 getGroup().cs = new HydrophobicColourScheme();
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387 protected void helixColour_actionPerformed(ActionEvent e)
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389 getGroup().cs = new HelixColourScheme();
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393 protected void strandColour_actionPerformed(ActionEvent e)
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395 getGroup().cs = new StrandColourScheme();
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399 protected void turnColour_actionPerformed(ActionEvent e)
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401 getGroup().cs = new TurnColourScheme();
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405 protected void buriedColour_actionPerformed(ActionEvent e)
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407 getGroup().cs = new BuriedColourScheme();
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411 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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413 getGroup().cs = new NucleotideColourScheme();
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419 protected void abovePIDColour_actionPerformed(ActionEvent e)
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421 SequenceGroup sg = getGroup();
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422 if (abovePIDColour.isSelected())
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424 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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425 ap.av.alignment.getWidth()));
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426 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
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427 if (sg.cs instanceof ResidueColourScheme)
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428 ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
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429 else if (sg.cs instanceof ScoreColourScheme)
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430 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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432 SliderPanel.showPIDSlider();
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436 else // remove PIDColouring
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438 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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439 rcs.setThreshold(0);
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448 protected void userDefinedColour_actionPerformed(ActionEvent e)
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450 new UserDefinedColours( ap, getGroup());
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453 protected void PIDColour_actionPerformed(ActionEvent e)
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455 SequenceGroup sg = getGroup();
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456 sg.cs = new PIDColourScheme();
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457 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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458 ap.av.alignment.getWidth()));
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462 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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464 SequenceGroup sg = getGroup();
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466 sg.cs = new Blosum62ColourScheme();
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468 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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469 ap.av.alignment.getWidth()));
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475 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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477 getGroup().cs = null;
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481 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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483 SequenceGroup sg = getGroup();
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485 if(conservationMenuItem.isSelected())
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488 Conservation c = new Conservation("Group",
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489 ResidueProperties.propHash, 3,
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491 ap.av.alignment.getWidth());
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494 c.verdict(false, ap.av.ConsPercGaps);
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495 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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500 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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501 SliderPanel.showConservationSlider();
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503 else // remove ConservationColouring
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505 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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513 protected void groupName_actionPerformed(ActionEvent e)
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515 SequenceGroup sg = getGroup();
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516 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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521 groupName.setText(reply);
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525 protected void analyze_actionPerformed(ActionEvent e)
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527 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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528 JInternalFrame frame = new JInternalFrame();
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529 cap.formatForOutput();
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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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