3 import jalview.datamodel.*;
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4 import jalview.analysis.*;
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5 import jalview.schemes.*;
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6 import javax.swing.*;
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7 import java.awt.event.*;
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11 public class PopupMenu extends JPopupMenu
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13 JMenu groupMenu = new JMenu();
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14 JMenuItem copyGroup = new JMenuItem();
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15 JMenuItem moveGroup = new JMenuItem();
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16 JMenuItem deleteSequences = new JMenuItem();
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17 JMenuItem analyze = new JMenuItem();
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18 JMenu defineMenu = new JMenu();
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19 JMenuItem groupName = new JMenuItem();
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20 JMenuItem groupAnnotation = new JMenuItem();
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21 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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22 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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23 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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24 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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25 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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26 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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27 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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28 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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29 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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30 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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31 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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32 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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33 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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34 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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38 JMenu sequenceMenu = new JMenu();
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39 JMenuItem sequenceName = new JMenuItem();
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40 JMenu residueMenu = new JMenu();
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41 JMenuItem annotateResidue = new JMenuItem();
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44 JMenuItem unGroupMenuItem = new JMenuItem();
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45 JMenuItem pdbMenuItem = new JMenuItem();
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47 public PopupMenu(AlignmentPanel ap, Sequence seq)
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49 ///////////////////////////////////////////////////////////
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50 // If this is activated from the sequence panel, the user may want to
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51 // edit or annotate a particular residue. Therefore display the residue menu
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53 // If from the IDPanel, we must display the sequence menu
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54 //////////////////////////////////////////////////////////
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59 ButtonGroup colours = new ButtonGroup();
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60 colours.add(noColourmenuItem);
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61 colours.add(clustalColour);
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62 colours.add(zappoColour);
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63 colours.add(taylorColour);
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64 colours.add(hydrophobicityColour);
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65 colours.add(helixColour);
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66 colours.add(strandColour);
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67 colours.add(turnColour);
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68 colours.add(buriedColour);
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69 colours.add(abovePIDColour);
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70 colours.add(userDefinedColour);
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71 colours.add(PIDColour);
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72 colours.add(BLOSUM62Colour);
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77 { e.printStackTrace(); }
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79 SequenceGroup sg = ap.av.getRubberbandGroup();
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82 groupName.setText(sg.getName());
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83 if(sg.cs instanceof ZappoColourScheme)
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84 zappoColour.setSelected(true);
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85 else if(sg.cs instanceof TaylorColourScheme)
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86 taylorColour.setSelected(true);
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87 else if (sg.cs instanceof PIDColourScheme)
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88 PIDColour.setSelected(true);
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89 else if (sg.cs instanceof Blosum62ColourScheme)
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90 BLOSUM62Colour.setSelected(true);
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91 else if (sg.cs instanceof UserColourScheme)
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92 userDefinedColour.setSelected(true);
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93 else if (sg.cs instanceof HydrophobicColourScheme)
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94 hydrophobicityColour.setSelected(true);
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95 else if (sg.cs instanceof HelixColourScheme)
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96 helixColour.setSelected(true);
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97 else if (sg.cs instanceof StrandColourScheme)
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98 strandColour.setSelected(true);
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99 else if (sg.cs instanceof TurnColourScheme)
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100 turnColour.setSelected(true);
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101 else if (sg.cs instanceof BuriedColourScheme)
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102 buriedColour.setSelected(true);
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103 else if (sg.cs instanceof ClustalxColourScheme)
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104 clustalColour.setSelected(true);
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106 noColourmenuItem.setSelected(true);
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108 if (sg.cs instanceof ConservationColourScheme)
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109 conservationMenuItem.setSelected(true);
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115 residueMenu.setVisible(false);
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116 sequenceName.setText( sequence.getName() );
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119 sequenceMenu.setVisible(false);
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122 private void jbInit() throws Exception
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124 groupMenu.setText("Group");
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125 copyGroup.setText("Copy region to new Alignment");
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126 copyGroup.addActionListener(new java.awt.event.ActionListener()
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128 public void actionPerformed(ActionEvent e)
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130 copyGroup_actionPerformed(e);
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133 moveGroup.setText("Move sequences to new Alignment");
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134 moveGroup.addActionListener(new java.awt.event.ActionListener()
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136 public void actionPerformed(ActionEvent e)
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138 moveGroup_actionPerformed(e);
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141 deleteSequences.setText("Delete sequences");
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142 deleteSequences.addActionListener(new java.awt.event.ActionListener()
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144 public void actionPerformed(ActionEvent e)
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146 deleteSequences_actionPerformed(e);
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149 analyze.setText("Analyze");
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150 analyze.addActionListener(new java.awt.event.ActionListener()
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152 public void actionPerformed(ActionEvent e)
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154 analyze_actionPerformed(e);
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157 defineMenu.setText("Define");
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158 groupName.setText("Name");
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159 groupName.addActionListener(new java.awt.event.ActionListener()
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161 public void actionPerformed(ActionEvent e)
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163 groupName_actionPerformed(e);
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166 groupAnnotation.setText("Annotation");
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167 groupAnnotation.addActionListener(new java.awt.event.ActionListener()
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169 public void actionPerformed(ActionEvent e)
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171 groupAnnotation_actionPerformed(e);
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174 sequenceMenu.setText("Sequence");
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175 sequenceName.setText("sequenceName");
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176 sequenceName.addActionListener(new java.awt.event.ActionListener()
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178 public void actionPerformed(ActionEvent e)
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180 sequenceName_actionPerformed(e);
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183 residueMenu.setText("Residue");
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184 annotateResidue.setText("annotate residue???");
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185 PIDColour.setFocusPainted(false);
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186 unGroupMenuItem.setText("Remove Group");
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187 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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189 public void actionPerformed(ActionEvent e)
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191 unGroupMenuItem_actionPerformed(e);
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194 pdbMenuItem.setText("View PDB structure");
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195 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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197 public void actionPerformed(ActionEvent e)
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199 pdbMenuItem_actionPerformed(e);
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203 this.add(sequenceMenu);
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204 this.add(residueMenu);
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205 groupMenu.add(defineMenu);
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206 groupMenu.add(unGroupMenuItem);
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207 groupMenu.addSeparator();
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208 groupMenu.add(copyGroup);
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209 groupMenu.add(moveGroup);
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210 groupMenu.add(deleteSequences);
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211 groupMenu.addSeparator();
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212 groupMenu.add(analyze);
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213 defineMenu.add(groupName);
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214 defineMenu.add(groupAnnotation);
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215 defineMenu.addSeparator();
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216 defineMenu.add(noColourmenuItem);
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217 defineMenu.add(clustalColour);
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218 defineMenu.add(zappoColour);
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219 defineMenu.add(taylorColour);
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220 defineMenu.add(hydrophobicityColour);
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221 defineMenu.add(helixColour);
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222 defineMenu.add(strandColour);
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223 defineMenu.add(turnColour);
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224 defineMenu.add(buriedColour);
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225 defineMenu.add(userDefinedColour);
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226 defineMenu.add(PIDColour);
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227 defineMenu.add(BLOSUM62Colour);
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228 defineMenu.addSeparator();
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229 defineMenu.add(abovePIDColour);
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230 defineMenu.add(conservationMenuItem);
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232 sequenceMenu.add(sequenceName);
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233 sequenceMenu.add(pdbMenuItem);
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234 residueMenu.add(annotateResidue);
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236 noColourmenuItem.setText("None");
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237 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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239 public void actionPerformed(ActionEvent e)
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241 noColourmenuItem_actionPerformed(e);
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245 clustalColour.setText("Clustalx colours");
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246 clustalColour.addActionListener(new java.awt.event.ActionListener()
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248 public void actionPerformed(ActionEvent e)
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250 clustalColour_actionPerformed(e);
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253 zappoColour.setText("Zappo colour scheme");
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254 zappoColour.addActionListener(new java.awt.event.ActionListener()
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256 public void actionPerformed(ActionEvent e)
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258 zappoColour_actionPerformed(e);
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261 taylorColour.setText("Taylor colour scheme");
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262 taylorColour.addActionListener(new java.awt.event.ActionListener()
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264 public void actionPerformed(ActionEvent e)
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266 taylorColour_actionPerformed(e);
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269 hydrophobicityColour.setText("By hydrophobicity");
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270 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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272 public void actionPerformed(ActionEvent e)
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274 hydrophobicityColour_actionPerformed(e);
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277 helixColour.setText("Helix propensity");
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278 helixColour.addActionListener(new java.awt.event.ActionListener()
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280 public void actionPerformed(ActionEvent e)
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282 helixColour_actionPerformed(e);
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285 strandColour.setText("Strand propensity");
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286 strandColour.addActionListener(new java.awt.event.ActionListener()
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288 public void actionPerformed(ActionEvent e)
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290 strandColour_actionPerformed(e);
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293 turnColour.setText("Turn propensity");
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294 turnColour.addActionListener(new java.awt.event.ActionListener()
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296 public void actionPerformed(ActionEvent e)
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298 turnColour_actionPerformed(e);
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301 buriedColour.setText("Buried index");
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302 buriedColour.addActionListener(new java.awt.event.ActionListener()
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304 public void actionPerformed(ActionEvent e)
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306 buriedColour_actionPerformed(e);
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309 abovePIDColour.setText("Above PID threshold only");
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310 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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312 public void actionPerformed(ActionEvent e)
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314 abovePIDColour_actionPerformed(e);
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317 userDefinedColour.setText("User defined colours");
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318 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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320 public void actionPerformed(ActionEvent e)
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322 userDefinedColour_actionPerformed(e);
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325 PIDColour.setText("Percentage Identity");
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326 PIDColour.addActionListener(new java.awt.event.ActionListener()
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328 public void actionPerformed(ActionEvent e)
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330 PIDColour_actionPerformed(e);
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333 BLOSUM62Colour.setText("BLOSUM62 score");
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334 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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336 public void actionPerformed(ActionEvent e)
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338 BLOSUM62Colour_actionPerformed(e);
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341 conservationMenuItem.setText("By conservation");
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342 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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344 public void actionPerformed(ActionEvent e)
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346 conservationMenuItem_actionPerformed(e);
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356 SequenceGroup sg = getGroup();
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357 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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359 superG.setSuperGroupProperties( sg );
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361 ap.seqPanel.seqCanvas.paintFlag=true;
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362 ap.seqPanel.repaint();
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365 protected void clustalColour_actionPerformed(ActionEvent e)
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367 SequenceGroup sg = getGroup();
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368 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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372 protected void zappoColour_actionPerformed(ActionEvent e)
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374 getGroup().cs = new ZappoColourScheme();
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378 protected void taylorColour_actionPerformed(ActionEvent e)
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380 getGroup().cs = new TaylorColourScheme();
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385 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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387 getGroup().cs = new HydrophobicColourScheme();
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391 protected void helixColour_actionPerformed(ActionEvent e)
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393 getGroup().cs = new HelixColourScheme();
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397 protected void strandColour_actionPerformed(ActionEvent e)
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399 getGroup().cs = new StrandColourScheme();
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403 protected void turnColour_actionPerformed(ActionEvent e)
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405 getGroup().cs = new TurnColourScheme();
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409 protected void buriedColour_actionPerformed(ActionEvent e)
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411 getGroup().cs = new BuriedColourScheme();
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416 protected void abovePIDColour_actionPerformed(ActionEvent e)
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418 Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
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422 protected void userDefinedColour_actionPerformed(ActionEvent e)
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424 JInternalFrame frame = new JInternalFrame();
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425 UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
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426 frame.setContentPane(chooser);
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427 Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
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428 frame.setResizable(false);
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429 frame.setIconifiable(false);
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430 frame.setMaximizable(false);
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434 protected void PIDColour_actionPerformed(ActionEvent e)
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439 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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441 getGroup().cs = new Blosum62ColourScheme(ap.av);
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446 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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448 getGroup().cs = null;
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452 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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454 SequenceGroup sg = getGroup();
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456 if(conservationMenuItem.isSelected())
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459 Conservation c = new Conservation("Group",
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460 ResidueProperties.propHash, 3,
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462 ap.av.alignment.getWidth());
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465 c.verdict(false, 100);
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466 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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471 Desktop.setConservationSliderSource(ap, ccs, sg.getName());
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473 else // remove ConservationColouring
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475 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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482 protected void groupAnnotation_actionPerformed(ActionEvent e)
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487 protected void groupName_actionPerformed(ActionEvent e)
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489 SequenceGroup sg = getGroup();
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490 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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495 groupName.setText(reply);
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498 protected void copyGroup_actionPerformed(ActionEvent e)
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500 SequenceGroup sg = ap.av.getRubberbandGroup();
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502 SequenceI[] s = new Sequence[sg.sequences.size()];
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503 for (int i=0; i < sg.sequences.size(); i++)
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505 s[i] = new Sequence( sg.getSequenceAt(i));
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506 s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
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508 AlignFrame af = new AlignFrame(new Alignment(s));
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509 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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510 if (newHeight > 500)
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512 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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515 protected void moveGroup_actionPerformed(ActionEvent e)
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517 SequenceGroup sg = ap.av.getRubberbandGroup();
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519 SequenceI[] s = new Sequence[sg.sequences.size()];
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521 for (int i=0; i < sg.sequences.size(); i++)
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522 s[i] = new Sequence( sg.getSequenceAt(i));
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524 AlignFrame af = new AlignFrame(new Alignment(s));
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525 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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528 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
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531 for (int i=0; i < sg.sequences.size(); i++)
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532 ap.av.alignment.deleteSequence(sg.getSequenceAt(i));
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535 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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536 ap.RefreshPanels();
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541 protected void deleteSequences_actionPerformed(ActionEvent e)
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543 SequenceGroup sg = ap.av.getRubberbandGroup();
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544 for (int i=0;i < sg.sequences.size(); i++)
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545 ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));
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547 ap.av.alignment.deleteGroup(sg);
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548 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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549 ap.RefreshPanels();
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553 protected void analyze_actionPerformed(ActionEvent e)
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555 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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556 JInternalFrame frame = new JInternalFrame();
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557 cap.formatForOutput();
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558 frame.setContentPane(cap);
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559 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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560 SequenceGroup sg = getGroup();
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561 StringBuffer sb = new StringBuffer();
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563 for(int i=0; i<sg.sequences.size(); i++)
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565 Sequence tmp = (Sequence)sg.sequences.get(i);
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566 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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570 sb.append("Something amazing will happen soon");
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571 cap.setText( sb.toString() );
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575 SequenceGroup getGroup()
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577 SequenceGroup sg = ap.av.getRubberbandGroup();
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579 // this method won't add a new group if it already exists
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580 ap.av.alignment.addGroup(sg);
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584 void sequenceName_actionPerformed(ActionEvent e)
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586 String id = sequence.getName();
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587 String s = (String)JOptionPane.showInternalInputDialog(
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589 "Edit sequence name",
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590 "Edit sequence name",
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591 JOptionPane.PLAIN_MESSAGE,
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598 sequence.setName(s);
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599 ap.RefreshPanels();
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604 void unGroupMenuItem_actionPerformed(ActionEvent e)
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606 SequenceGroup sg = ap.av.getRubberbandGroup();
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607 ap.av.alignment.deleteGroup(sg);
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608 ap.av.setRubberbandGroup(null);
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609 ap.RefreshPanels();
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612 void pdbMenuItem_actionPerformed(ActionEvent e)
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614 if(sequence.getPDBId()==null)
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619 EBIFetchClient ebi = new EBIFetchClient();
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620 String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
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622 PDBfile pdb = new PDBfile(result);
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623 sequence.setPDBfile(pdb);
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625 ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;
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626 ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;
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627 // ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();
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629 rotCanvas rc = new rotCanvas(pdb);
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630 JInternalFrame frame = new JInternalFrame();
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631 frame.setContentPane(rc);
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632 Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
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634 catch (Exception ex)
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636 ex.printStackTrace();
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