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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41 public PopupMenu(AlignmentPanel ap, Sequence seq)
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43 ///////////////////////////////////////////////////////////
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44 // If this is activated from the sequence panel, the user may want to
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45 // edit or annotate a particular residue. Therefore display the residue menu
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47 // If from the IDPanel, we must display the sequence menu
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48 //////////////////////////////////////////////////////////
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53 ButtonGroup colours = new ButtonGroup();
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54 colours.add(noColourmenuItem);
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55 colours.add(clustalColour);
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56 colours.add(zappoColour);
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57 colours.add(taylorColour);
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58 colours.add(hydrophobicityColour);
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59 colours.add(helixColour);
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60 colours.add(strandColour);
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61 colours.add(turnColour);
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62 colours.add(buriedColour);
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63 colours.add(abovePIDColour);
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64 colours.add(userDefinedColour);
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65 colours.add(PIDColour);
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66 colours.add(BLOSUM62Colour);
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71 { e.printStackTrace(); }
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73 SequenceGroup sg = ap.av.getSelectionGroup();
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76 groupName.setText(sg.getName());
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77 if(sg.cs instanceof ZappoColourScheme)
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78 zappoColour.setSelected(true);
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79 else if(sg.cs instanceof TaylorColourScheme)
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80 taylorColour.setSelected(true);
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81 else if (sg.cs instanceof PIDColourScheme)
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82 PIDColour.setSelected(true);
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83 else if (sg.cs instanceof Blosum62ColourScheme)
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84 BLOSUM62Colour.setSelected(true);
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85 else if (sg.cs instanceof UserColourScheme)
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86 userDefinedColour.setSelected(true);
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87 else if (sg.cs instanceof HydrophobicColourScheme)
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88 hydrophobicityColour.setSelected(true);
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89 else if (sg.cs instanceof HelixColourScheme)
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90 helixColour.setSelected(true);
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91 else if (sg.cs instanceof StrandColourScheme)
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92 strandColour.setSelected(true);
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93 else if (sg.cs instanceof TurnColourScheme)
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94 turnColour.setSelected(true);
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95 else if (sg.cs instanceof BuriedColourScheme)
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96 buriedColour.setSelected(true);
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97 else if (sg.cs instanceof ClustalxColourScheme)
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98 clustalColour.setSelected(true);
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100 noColourmenuItem.setSelected(true);
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102 if (sg.cs instanceof ConservationColourScheme)
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103 conservationMenuItem.setSelected(true);
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106 if( !ap.av.alignment.getGroups().contains(sg))
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107 unGroupMenuItem.setVisible(false);
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110 sequenceMenu.setVisible(false);
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113 private void jbInit() throws Exception
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115 groupMenu.setText("Group");
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116 groupMenu.setText("Define");
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117 groupName.setText("Name");
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118 groupName.addActionListener(new java.awt.event.ActionListener()
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120 public void actionPerformed(ActionEvent e)
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122 groupName_actionPerformed(e);
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125 sequenceMenu.setText("Sequence");
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126 sequenceName.setText("Edit name");
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127 sequenceName.addActionListener(new java.awt.event.ActionListener()
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129 public void actionPerformed(ActionEvent e)
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131 sequenceName_actionPerformed(e);
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134 PIDColour.setFocusPainted(false);
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135 unGroupMenuItem.setText("Remove Group");
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136 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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138 public void actionPerformed(ActionEvent e)
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140 unGroupMenuItem_actionPerformed(e);
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143 pdbMenuItem.setText("View PDB structure");
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144 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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146 public void actionPerformed(ActionEvent e)
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148 pdbMenuItem_actionPerformed(e);
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151 outline.setText("Border colour");
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152 outline.addActionListener(new java.awt.event.ActionListener()
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154 public void actionPerformed(ActionEvent e)
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156 outline_actionPerformed(e);
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159 nucleotideMenuItem.setText("Nucleotide");
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160 nucleotideMenuItem.addActionListener(new ActionListener()
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162 public void actionPerformed(ActionEvent e)
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164 nucleotideMenuItem_actionPerformed(e);
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169 groupMenu.add(groupName);
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170 groupMenu.addSeparator();
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171 groupMenu.add(unGroupMenuItem);
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172 groupMenu.addSeparator();
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173 groupMenu.add(outline);
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174 groupMenu.addSeparator();
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175 groupMenu.add(noColourmenuItem);
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176 groupMenu.add(clustalColour);
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177 groupMenu.add(BLOSUM62Colour);
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178 groupMenu.add(PIDColour);
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180 groupMenu.add(zappoColour);
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181 groupMenu.add(taylorColour);
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182 groupMenu.add(hydrophobicityColour);
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183 groupMenu.add(helixColour);
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184 groupMenu.add(strandColour);
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185 groupMenu.add(turnColour);
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186 groupMenu.add(buriedColour);
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187 groupMenu.add(nucleotideMenuItem);
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189 groupMenu.add(userDefinedColour);
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191 groupMenu.addSeparator();
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192 groupMenu.add(abovePIDColour);
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193 groupMenu.add(conservationMenuItem);
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195 sequenceMenu.add(sequenceName);
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196 sequenceMenu.add(pdbMenuItem);
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197 noColourmenuItem.setText("None");
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198 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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200 public void actionPerformed(ActionEvent e)
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202 noColourmenuItem_actionPerformed(e);
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206 clustalColour.setText("Clustalx colours");
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207 clustalColour.addActionListener(new java.awt.event.ActionListener()
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209 public void actionPerformed(ActionEvent e)
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211 clustalColour_actionPerformed(e);
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214 zappoColour.setText("Zappo");
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215 zappoColour.addActionListener(new java.awt.event.ActionListener()
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217 public void actionPerformed(ActionEvent e)
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219 zappoColour_actionPerformed(e);
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222 taylorColour.setText("Taylor");
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223 taylorColour.addActionListener(new java.awt.event.ActionListener()
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225 public void actionPerformed(ActionEvent e)
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227 taylorColour_actionPerformed(e);
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230 hydrophobicityColour.setText("Hydrophobicity");
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231 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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233 public void actionPerformed(ActionEvent e)
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235 hydrophobicityColour_actionPerformed(e);
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238 helixColour.setText("Helix propensity");
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239 helixColour.addActionListener(new java.awt.event.ActionListener()
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241 public void actionPerformed(ActionEvent e)
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243 helixColour_actionPerformed(e);
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246 strandColour.setText("Strand propensity");
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247 strandColour.addActionListener(new java.awt.event.ActionListener()
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249 public void actionPerformed(ActionEvent e)
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251 strandColour_actionPerformed(e);
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254 turnColour.setText("Turn propensity");
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255 turnColour.addActionListener(new java.awt.event.ActionListener()
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257 public void actionPerformed(ActionEvent e)
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259 turnColour_actionPerformed(e);
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262 buriedColour.setText("Buried Index");
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263 buriedColour.addActionListener(new java.awt.event.ActionListener()
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265 public void actionPerformed(ActionEvent e)
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267 buriedColour_actionPerformed(e);
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270 abovePIDColour.setText("Above % Identity");
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271 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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273 public void actionPerformed(ActionEvent e)
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275 abovePIDColour_actionPerformed(e);
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278 userDefinedColour.setText("User Defined");
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279 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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281 public void actionPerformed(ActionEvent e)
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283 userDefinedColour_actionPerformed(e);
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286 PIDColour.setText("Percentage Identity");
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287 PIDColour.addActionListener(new java.awt.event.ActionListener()
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289 public void actionPerformed(ActionEvent e)
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291 PIDColour_actionPerformed(e);
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294 BLOSUM62Colour.setText("BLOSUM62");
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295 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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297 public void actionPerformed(ActionEvent e)
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299 BLOSUM62Colour_actionPerformed(e);
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302 conservationMenuItem.setText("Conservation");
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303 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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305 public void actionPerformed(ActionEvent e)
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307 conservationMenuItem_actionPerformed(e);
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317 SequenceGroup sg = getGroup();
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318 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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320 superG.setSuperGroupProperties( sg );
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322 ap.seqPanel.repaint();
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325 protected void clustalColour_actionPerformed(ActionEvent e)
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327 SequenceGroup sg = getGroup();
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328 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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332 protected void zappoColour_actionPerformed(ActionEvent e)
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334 getGroup().cs = new ZappoColourScheme();
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338 protected void taylorColour_actionPerformed(ActionEvent e)
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340 getGroup().cs = new TaylorColourScheme();
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345 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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347 getGroup().cs = new HydrophobicColourScheme();
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351 protected void helixColour_actionPerformed(ActionEvent e)
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353 getGroup().cs = new HelixColourScheme();
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357 protected void strandColour_actionPerformed(ActionEvent e)
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359 getGroup().cs = new StrandColourScheme();
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363 protected void turnColour_actionPerformed(ActionEvent e)
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365 getGroup().cs = new TurnColourScheme();
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369 protected void buriedColour_actionPerformed(ActionEvent e)
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371 getGroup().cs = new BuriedColourScheme();
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375 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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377 getGroup().cs = new NucleotideColourScheme();
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383 protected void abovePIDColour_actionPerformed(ActionEvent e)
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385 SequenceGroup sg = getGroup();
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386 if (abovePIDColour.isSelected())
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388 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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389 ap.av.alignment.getWidth()));
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390 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
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391 if (sg.cs instanceof ResidueColourScheme)
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392 ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
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393 else if (sg.cs instanceof ScoreColourScheme)
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394 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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396 SliderPanel.showPIDSlider();
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400 else // remove PIDColouring
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402 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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403 rcs.setThreshold(0);
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412 protected void userDefinedColour_actionPerformed(ActionEvent e)
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414 UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());
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417 protected void PIDColour_actionPerformed(ActionEvent e)
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422 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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424 SequenceGroup sg = getGroup();
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426 sg.cs = new Blosum62ColourScheme();
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428 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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429 ap.av.alignment.getWidth()));
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435 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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437 getGroup().cs = null;
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441 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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443 SequenceGroup sg = getGroup();
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445 if(conservationMenuItem.isSelected())
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448 Conservation c = new Conservation("Group",
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449 ResidueProperties.propHash, 3,
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451 ap.av.alignment.getWidth());
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454 c.verdict(false, ap.av.ConsPercGaps);
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455 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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460 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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461 SliderPanel.showConservationSlider();
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463 else // remove ConservationColouring
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465 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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472 protected void groupAnnotation_actionPerformed(ActionEvent e)
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477 protected void groupName_actionPerformed(ActionEvent e)
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479 SequenceGroup sg = getGroup();
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480 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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485 groupName.setText(reply);
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489 protected void analyze_actionPerformed(ActionEvent e)
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491 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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492 JInternalFrame frame = new JInternalFrame();
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493 cap.formatForOutput();
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494 frame.setContentPane(cap);
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495 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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496 SequenceGroup sg = getGroup();
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497 StringBuffer sb = new StringBuffer();
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499 for(int i=0; i<sg.sequences.size(); i++)
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501 Sequence tmp = (Sequence)sg.sequences.get(i);
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502 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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506 sb.append("Something amazing will happen soon");
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507 cap.setText( sb.toString() );
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511 SequenceGroup getGroup()
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513 SequenceGroup sg = ap.av.getSelectionGroup();
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515 // this method won't add a new group if it already exists
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516 ap.av.alignment.addGroup(sg);
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521 void sequenceName_actionPerformed(ActionEvent e)
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523 String id = sequence.getName();
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524 String s = (String)JOptionPane.showInternalInputDialog(
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526 "Edit sequence name",
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527 "Edit sequence name ("+sequence.getName()+")",
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528 JOptionPane.PLAIN_MESSAGE,
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535 sequence.setName(s);
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541 void unGroupMenuItem_actionPerformed(ActionEvent e)
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543 SequenceGroup sg = ap.av.getSelectionGroup();
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544 ap.av.alignment.deleteGroup(sg);
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545 ap.av.setSelectionGroup(null);
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549 void pdbMenuItem_actionPerformed(ActionEvent e)
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551 if(sequence.getPDBId()==null)
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556 EBIFetchClient ebi = new EBIFetchClient();
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557 String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
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559 System.out.println("Got "+ sequence.getPDBId() );
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560 PDBfile pdb = new PDBfile(result);
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562 rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);
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563 JInternalFrame frame = new JInternalFrame();
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564 frame.setContentPane(rc);
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565 Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
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567 catch (Exception ex)
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569 ex.printStackTrace();
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573 protected void outline_actionPerformed(ActionEvent e)
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575 SequenceGroup sg = getGroup();
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576 Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
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578 sg.setOutlineColour(col);
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