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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114 residueMenu.setVisible(false);
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116 sequenceMenu.setVisible(false);
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119 private void jbInit() throws Exception
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121 groupMenu.setText("Group");
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122 copyGroup.setText("Copy region to new Alignment");
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123 copyGroup.addActionListener(new java.awt.event.ActionListener()
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125 public void actionPerformed(ActionEvent e)
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127 copyGroup_actionPerformed(e);
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130 moveGroup.setText("Move sequences to new Alignment");
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131 moveGroup.addActionListener(new java.awt.event.ActionListener()
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133 public void actionPerformed(ActionEvent e)
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135 moveGroup_actionPerformed(e);
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138 deleteSequences.setText("Delete sequences");
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139 deleteSequences.addActionListener(new java.awt.event.ActionListener()
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141 public void actionPerformed(ActionEvent e)
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143 deleteSequences_actionPerformed(e);
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146 analyze.setText("Analyze");
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147 analyze.addActionListener(new java.awt.event.ActionListener()
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149 public void actionPerformed(ActionEvent e)
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151 analyze_actionPerformed(e);
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154 defineMenu.setText("Define");
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155 groupName.setText("Name");
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156 groupName.addActionListener(new java.awt.event.ActionListener()
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158 public void actionPerformed(ActionEvent e)
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160 groupName_actionPerformed(e);
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163 groupAnnotation.setText("Annotation");
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164 groupAnnotation.addActionListener(new java.awt.event.ActionListener()
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166 public void actionPerformed(ActionEvent e)
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168 groupAnnotation_actionPerformed(e);
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171 sequenceMenu.setText("Sequence");
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172 sequenceName.setText("Edit name");
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173 sequenceName.addActionListener(new java.awt.event.ActionListener()
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175 public void actionPerformed(ActionEvent e)
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177 sequenceName_actionPerformed(e);
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180 residueMenu.setText("Residue");
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181 annotateResidue.setText("annotate residue???");
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182 PIDColour.setFocusPainted(false);
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183 unGroupMenuItem.setText("Remove Group");
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184 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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186 public void actionPerformed(ActionEvent e)
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188 unGroupMenuItem_actionPerformed(e);
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191 pdbMenuItem.setText("View PDB structure");
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192 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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194 public void actionPerformed(ActionEvent e)
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196 pdbMenuItem_actionPerformed(e);
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200 this.add(sequenceMenu);
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201 this.add(residueMenu);
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202 groupMenu.add(defineMenu);
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203 groupMenu.add(unGroupMenuItem);
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204 groupMenu.addSeparator();
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205 groupMenu.add(copyGroup);
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206 groupMenu.add(moveGroup);
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207 groupMenu.add(deleteSequences);
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208 groupMenu.addSeparator();
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209 groupMenu.add(analyze);
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210 defineMenu.add(groupName);
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211 defineMenu.add(groupAnnotation);
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212 defineMenu.addSeparator();
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213 defineMenu.add(noColourmenuItem);
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214 defineMenu.add(clustalColour);
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215 defineMenu.add(zappoColour);
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216 defineMenu.add(taylorColour);
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217 defineMenu.add(hydrophobicityColour);
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218 defineMenu.add(helixColour);
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219 defineMenu.add(strandColour);
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220 defineMenu.add(turnColour);
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221 defineMenu.add(buriedColour);
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222 defineMenu.add(userDefinedColour);
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223 defineMenu.add(PIDColour);
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224 defineMenu.add(BLOSUM62Colour);
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225 defineMenu.addSeparator();
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226 defineMenu.add(abovePIDColour);
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227 defineMenu.add(conservationMenuItem);
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229 sequenceMenu.add(sequenceName);
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230 sequenceMenu.add(pdbMenuItem);
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231 residueMenu.add(annotateResidue);
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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 colour scheme");
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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 colour scheme");
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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("By 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 PID threshold only");
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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 colours");
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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 score");
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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("By 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.seqCanvas.paintFlag=true;
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359 ap.seqPanel.repaint();
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362 protected void clustalColour_actionPerformed(ActionEvent e)
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364 SequenceGroup sg = getGroup();
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365 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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369 protected void zappoColour_actionPerformed(ActionEvent e)
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371 getGroup().cs = new ZappoColourScheme();
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375 protected void taylorColour_actionPerformed(ActionEvent e)
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377 getGroup().cs = new TaylorColourScheme();
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382 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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384 getGroup().cs = new HydrophobicColourScheme();
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388 protected void helixColour_actionPerformed(ActionEvent e)
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390 getGroup().cs = new HelixColourScheme();
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394 protected void strandColour_actionPerformed(ActionEvent e)
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396 getGroup().cs = new StrandColourScheme();
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400 protected void turnColour_actionPerformed(ActionEvent e)
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402 getGroup().cs = new TurnColourScheme();
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406 protected void buriedColour_actionPerformed(ActionEvent e)
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408 getGroup().cs = new BuriedColourScheme();
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413 protected void abovePIDColour_actionPerformed(ActionEvent e)
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415 Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
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419 protected void userDefinedColour_actionPerformed(ActionEvent e)
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421 JInternalFrame frame = new JInternalFrame();
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422 UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
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423 frame.setContentPane(chooser);
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424 Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
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425 frame.setResizable(false);
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426 frame.setIconifiable(false);
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427 frame.setMaximizable(false);
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431 protected void PIDColour_actionPerformed(ActionEvent e)
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436 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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438 getGroup().cs = new Blosum62ColourScheme(ap.av);
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443 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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445 getGroup().cs = null;
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449 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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451 SequenceGroup sg = getGroup();
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453 if(conservationMenuItem.isSelected())
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456 Conservation c = new Conservation("Group",
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457 ResidueProperties.propHash, 3,
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459 ap.av.alignment.getWidth());
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462 c.verdict(false, 100);
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463 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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468 Desktop.setConservationSliderSource(ap, ccs, sg.getName());
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470 else // remove ConservationColouring
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472 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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479 protected void groupAnnotation_actionPerformed(ActionEvent e)
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484 protected void groupName_actionPerformed(ActionEvent e)
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486 SequenceGroup sg = getGroup();
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487 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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492 groupName.setText(reply);
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495 protected void copyGroup_actionPerformed(ActionEvent e)
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497 SequenceGroup sg = ap.av.getRubberbandGroup();
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499 SequenceI[] s = new Sequence[sg.sequences.size()];
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500 for (int i=0; i < sg.sequences.size(); i++)
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502 s[i] = new Sequence( sg.getSequenceAt(i));
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503 s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
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505 AlignFrame af = new AlignFrame(new Alignment(s));
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506 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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507 if (newHeight > 500)
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509 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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512 protected void moveGroup_actionPerformed(ActionEvent e)
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514 SequenceGroup sg = ap.av.getRubberbandGroup();
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516 SequenceI[] s = new Sequence[sg.sequences.size()];
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518 for (int i=0; i < sg.sequences.size(); i++)
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519 s[i] = new Sequence( sg.getSequenceAt(i));
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521 AlignFrame af = new AlignFrame(new Alignment(s));
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522 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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525 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
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528 for (int i=0; i < sg.sequences.size(); i++)
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529 ap.av.alignment.deleteSequence(sg.getSequenceAt(i));
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532 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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533 ap.RefreshPanels();
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538 protected void deleteSequences_actionPerformed(ActionEvent e)
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540 SequenceGroup sg = ap.av.getRubberbandGroup();
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541 for (int i=0;i < sg.sequences.size(); i++)
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542 ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));
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544 ap.av.alignment.deleteGroup(sg);
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545 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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546 ap.RefreshPanels();
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550 protected void analyze_actionPerformed(ActionEvent e)
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552 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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553 JInternalFrame frame = new JInternalFrame();
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554 cap.formatForOutput();
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555 frame.setContentPane(cap);
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556 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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557 SequenceGroup sg = getGroup();
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558 StringBuffer sb = new StringBuffer();
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560 for(int i=0; i<sg.sequences.size(); i++)
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562 Sequence tmp = (Sequence)sg.sequences.get(i);
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563 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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567 sb.append("Something amazing will happen soon");
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568 cap.setText( sb.toString() );
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572 SequenceGroup getGroup()
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574 SequenceGroup sg = ap.av.getRubberbandGroup();
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576 // this method won't add a new group if it already exists
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577 ap.av.alignment.addGroup(sg);
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581 void sequenceName_actionPerformed(ActionEvent e)
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583 String id = sequence.getName();
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584 String s = (String)JOptionPane.showInternalInputDialog(
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586 "Edit sequence name",
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587 "Edit sequence name ("+sequence.getName()+")",
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588 JOptionPane.PLAIN_MESSAGE,
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595 sequence.setName(s);
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596 ap.RefreshPanels();
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601 void unGroupMenuItem_actionPerformed(ActionEvent e)
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603 SequenceGroup sg = ap.av.getRubberbandGroup();
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604 ap.av.alignment.deleteGroup(sg);
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605 ap.av.setRubberbandGroup(null);
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606 ap.RefreshPanels();
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609 void pdbMenuItem_actionPerformed(ActionEvent e)
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611 if(sequence.getPDBId()==null)
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616 EBIFetchClient ebi = new EBIFetchClient();
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617 String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
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619 PDBfile pdb = new PDBfile(result);
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620 sequence.setPDBfile(pdb);
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622 ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;
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623 ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;
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624 // ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();
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626 rotCanvas rc = new rotCanvas(pdb);
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627 JInternalFrame frame = new JInternalFrame();
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628 frame.setContentPane(rc);
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629 Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
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631 catch (Exception ex)
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633 ex.printStackTrace();
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