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 analyze = new JMenuItem();
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16 JMenu defineMenu = new JMenu();
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17 JMenuItem groupName = new JMenuItem();
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18 JMenuItem groupAnnotation = new JMenuItem();
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19 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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20 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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21 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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22 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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23 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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24 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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25 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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26 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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27 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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28 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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29 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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30 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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31 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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32 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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36 JMenu sequenceMenu = new JMenu();
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37 JMenuItem sequenceName = new JMenuItem();
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38 JMenu residueMenu = new JMenu();
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39 JMenuItem annotateResidue = new JMenuItem();
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42 JMenuItem unGroupMenuItem = new JMenuItem();
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43 JMenuItem pdbMenuItem = new JMenuItem();
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44 JMenuItem outline = new JMenuItem();
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46 public PopupMenu(AlignmentPanel ap, Sequence seq)
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48 ///////////////////////////////////////////////////////////
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49 // If this is activated from the sequence panel, the user may want to
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50 // edit or annotate a particular residue. Therefore display the residue menu
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52 // If from the IDPanel, we must display the sequence menu
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53 //////////////////////////////////////////////////////////
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58 ButtonGroup colours = new ButtonGroup();
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59 colours.add(noColourmenuItem);
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60 colours.add(clustalColour);
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61 colours.add(zappoColour);
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62 colours.add(taylorColour);
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63 colours.add(hydrophobicityColour);
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64 colours.add(helixColour);
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65 colours.add(strandColour);
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66 colours.add(turnColour);
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67 colours.add(buriedColour);
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68 colours.add(abovePIDColour);
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69 colours.add(userDefinedColour);
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70 colours.add(PIDColour);
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71 colours.add(BLOSUM62Colour);
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76 { e.printStackTrace(); }
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78 SequenceGroup sg = ap.av.getSelectionGroup();
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81 groupName.setText(sg.getName());
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82 if(sg.cs instanceof ZappoColourScheme)
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83 zappoColour.setSelected(true);
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84 else if(sg.cs instanceof TaylorColourScheme)
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85 taylorColour.setSelected(true);
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86 else if (sg.cs instanceof PIDColourScheme)
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87 PIDColour.setSelected(true);
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88 else if (sg.cs instanceof Blosum62ColourScheme)
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89 BLOSUM62Colour.setSelected(true);
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90 else if (sg.cs instanceof UserColourScheme)
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91 userDefinedColour.setSelected(true);
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92 else if (sg.cs instanceof HydrophobicColourScheme)
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93 hydrophobicityColour.setSelected(true);
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94 else if (sg.cs instanceof HelixColourScheme)
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95 helixColour.setSelected(true);
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96 else if (sg.cs instanceof StrandColourScheme)
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97 strandColour.setSelected(true);
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98 else if (sg.cs instanceof TurnColourScheme)
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99 turnColour.setSelected(true);
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100 else if (sg.cs instanceof BuriedColourScheme)
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101 buriedColour.setSelected(true);
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102 else if (sg.cs instanceof ClustalxColourScheme)
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103 clustalColour.setSelected(true);
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105 noColourmenuItem.setSelected(true);
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107 if (sg.cs instanceof ConservationColourScheme)
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108 conservationMenuItem.setSelected(true);
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113 residueMenu.setVisible(false);
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115 sequenceMenu.setVisible(false);
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118 private void jbInit() throws Exception
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120 groupMenu.setText("Group");
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121 analyze.setText("Analyze");
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122 analyze.addActionListener(new java.awt.event.ActionListener()
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124 public void actionPerformed(ActionEvent e)
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126 analyze_actionPerformed(e);
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129 defineMenu.setText("Define");
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130 groupName.setText("Name");
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131 groupName.addActionListener(new java.awt.event.ActionListener()
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133 public void actionPerformed(ActionEvent e)
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135 groupName_actionPerformed(e);
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138 groupAnnotation.setEnabled(false);
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139 groupAnnotation.setText("Annotation");
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140 groupAnnotation.addActionListener(new java.awt.event.ActionListener()
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142 public void actionPerformed(ActionEvent e)
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144 groupAnnotation_actionPerformed(e);
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147 sequenceMenu.setText("Sequence");
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148 sequenceName.setText("Edit name");
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149 sequenceName.addActionListener(new java.awt.event.ActionListener()
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151 public void actionPerformed(ActionEvent e)
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153 sequenceName_actionPerformed(e);
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156 residueMenu.setText("Residue");
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157 annotateResidue.setEnabled(false);
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158 annotateResidue.setActionCommand("annotate residue");
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159 annotateResidue.setText("annotate residue???");
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160 PIDColour.setFocusPainted(false);
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161 unGroupMenuItem.setText("Remove Group");
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162 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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164 public void actionPerformed(ActionEvent e)
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166 unGroupMenuItem_actionPerformed(e);
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169 pdbMenuItem.setText("View PDB structure");
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170 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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172 public void actionPerformed(ActionEvent e)
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174 pdbMenuItem_actionPerformed(e);
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177 outline.setText("Border colour");
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178 outline.addActionListener(new java.awt.event.ActionListener()
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180 public void actionPerformed(ActionEvent e)
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182 outline_actionPerformed(e);
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186 this.add(sequenceMenu);
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187 this.add(residueMenu);
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188 groupMenu.add(defineMenu);
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189 groupMenu.add(unGroupMenuItem);
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190 groupMenu.addSeparator();
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191 groupMenu.add(analyze);
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192 defineMenu.add(groupName);
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193 defineMenu.add(groupAnnotation);
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194 defineMenu.addSeparator();
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195 defineMenu.add(outline);
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196 defineMenu.addSeparator();
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197 defineMenu.add(noColourmenuItem);
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198 defineMenu.add(clustalColour);
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199 defineMenu.add(zappoColour);
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200 defineMenu.add(taylorColour);
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201 defineMenu.add(hydrophobicityColour);
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202 defineMenu.add(helixColour);
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203 defineMenu.add(strandColour);
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204 defineMenu.add(turnColour);
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205 defineMenu.add(buriedColour);
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206 defineMenu.add(userDefinedColour);
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207 defineMenu.add(PIDColour);
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208 defineMenu.add(BLOSUM62Colour);
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209 defineMenu.addSeparator();
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210 defineMenu.add(abovePIDColour);
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211 defineMenu.add(conservationMenuItem);
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213 sequenceMenu.add(sequenceName);
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214 sequenceMenu.add(pdbMenuItem);
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215 residueMenu.add(annotateResidue);
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217 noColourmenuItem.setText("None");
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218 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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220 public void actionPerformed(ActionEvent e)
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222 noColourmenuItem_actionPerformed(e);
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226 clustalColour.setText("Clustalx colours");
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227 clustalColour.addActionListener(new java.awt.event.ActionListener()
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229 public void actionPerformed(ActionEvent e)
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231 clustalColour_actionPerformed(e);
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234 zappoColour.setText("Zappo colour scheme");
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235 zappoColour.addActionListener(new java.awt.event.ActionListener()
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237 public void actionPerformed(ActionEvent e)
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239 zappoColour_actionPerformed(e);
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242 taylorColour.setText("Taylor colour scheme");
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243 taylorColour.addActionListener(new java.awt.event.ActionListener()
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245 public void actionPerformed(ActionEvent e)
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247 taylorColour_actionPerformed(e);
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250 hydrophobicityColour.setText("By hydrophobicity");
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251 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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253 public void actionPerformed(ActionEvent e)
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255 hydrophobicityColour_actionPerformed(e);
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258 helixColour.setText("Helix propensity");
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259 helixColour.addActionListener(new java.awt.event.ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 helixColour_actionPerformed(e);
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266 strandColour.setText("Strand propensity");
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267 strandColour.addActionListener(new java.awt.event.ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 strandColour_actionPerformed(e);
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274 turnColour.setText("Turn propensity");
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275 turnColour.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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279 turnColour_actionPerformed(e);
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282 buriedColour.setText("Buried index");
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283 buriedColour.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 buriedColour_actionPerformed(e);
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290 abovePIDColour.setText("Above PID threshold only");
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291 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 abovePIDColour_actionPerformed(e);
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298 userDefinedColour.setText("User defined colours");
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299 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 userDefinedColour_actionPerformed(e);
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306 PIDColour.setText("Percentage Identity");
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307 PIDColour.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 PIDColour_actionPerformed(e);
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314 BLOSUM62Colour.setText("BLOSUM62 score");
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315 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 BLOSUM62Colour_actionPerformed(e);
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322 conservationMenuItem.setText("By conservation");
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323 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 conservationMenuItem_actionPerformed(e);
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337 SequenceGroup sg = getGroup();
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338 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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340 superG.setSuperGroupProperties( sg );
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342 ap.seqPanel.repaint();
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345 protected void clustalColour_actionPerformed(ActionEvent e)
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347 SequenceGroup sg = getGroup();
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348 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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352 protected void zappoColour_actionPerformed(ActionEvent e)
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354 getGroup().cs = new ZappoColourScheme();
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358 protected void taylorColour_actionPerformed(ActionEvent e)
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360 getGroup().cs = new TaylorColourScheme();
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365 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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367 getGroup().cs = new HydrophobicColourScheme();
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371 protected void helixColour_actionPerformed(ActionEvent e)
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373 getGroup().cs = new HelixColourScheme();
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377 protected void strandColour_actionPerformed(ActionEvent e)
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379 getGroup().cs = new StrandColourScheme();
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383 protected void turnColour_actionPerformed(ActionEvent e)
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385 getGroup().cs = new TurnColourScheme();
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389 protected void buriedColour_actionPerformed(ActionEvent e)
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391 getGroup().cs = new BuriedColourScheme();
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396 protected void abovePIDColour_actionPerformed(ActionEvent e)
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398 SequenceGroup sg = getGroup();
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399 if (abovePIDColour.isSelected())
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401 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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402 ap.av.alignment.getWidth()));
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403 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
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404 if (sg.cs instanceof ResidueColourScheme)
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405 ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
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406 else if (sg.cs instanceof ScoreColourScheme)
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407 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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409 SliderPanel.showPIDSlider();
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413 else // remove PIDColouring
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415 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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416 rcs.setThreshold(0);
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425 protected void userDefinedColour_actionPerformed(ActionEvent e)
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427 JInternalFrame frame = new JInternalFrame();
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428 UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
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429 frame.setContentPane(chooser);
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430 Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
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431 frame.setResizable(false);
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432 frame.setIconifiable(false);
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433 frame.setMaximizable(false);
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437 protected void PIDColour_actionPerformed(ActionEvent e)
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442 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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444 SequenceGroup sg = getGroup();
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446 sg.cs = new Blosum62ColourScheme();
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448 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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449 ap.av.alignment.getWidth()));
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455 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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457 getGroup().cs = null;
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461 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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463 SequenceGroup sg = getGroup();
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465 if(conservationMenuItem.isSelected())
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468 Conservation c = new Conservation("Group",
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469 ResidueProperties.propHash, 3,
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471 ap.av.alignment.getWidth());
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474 c.verdict(false, ap.av.ConsPercGaps);
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475 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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480 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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481 SliderPanel.showConservationSlider();
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483 else // remove ConservationColouring
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485 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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492 protected void groupAnnotation_actionPerformed(ActionEvent e)
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497 protected void groupName_actionPerformed(ActionEvent e)
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499 SequenceGroup sg = getGroup();
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500 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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505 groupName.setText(reply);
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509 protected void analyze_actionPerformed(ActionEvent e)
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511 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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512 JInternalFrame frame = new JInternalFrame();
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513 cap.formatForOutput();
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514 frame.setContentPane(cap);
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515 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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516 SequenceGroup sg = getGroup();
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517 StringBuffer sb = new StringBuffer();
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519 for(int i=0; i<sg.sequences.size(); i++)
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521 Sequence tmp = (Sequence)sg.sequences.get(i);
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522 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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526 sb.append("Something amazing will happen soon");
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527 cap.setText( sb.toString() );
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531 SequenceGroup getGroup()
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533 SequenceGroup sg = ap.av.getSelectionGroup();
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535 // this method won't add a new group if it already exists
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536 ap.av.alignment.addGroup(sg);
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541 void sequenceName_actionPerformed(ActionEvent e)
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543 String id = sequence.getName();
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544 String s = (String)JOptionPane.showInternalInputDialog(
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546 "Edit sequence name",
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547 "Edit sequence name ("+sequence.getName()+")",
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548 JOptionPane.PLAIN_MESSAGE,
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555 sequence.setName(s);
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561 void unGroupMenuItem_actionPerformed(ActionEvent e)
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563 SequenceGroup sg = ap.av.getSelectionGroup();
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564 ap.av.alignment.deleteGroup(sg);
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565 ap.av.setSelectionGroup(null);
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569 void pdbMenuItem_actionPerformed(ActionEvent e)
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571 if(sequence.getPDBId()==null)
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576 EBIFetchClient ebi = new EBIFetchClient();
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577 String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
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579 PDBfile pdb = new PDBfile(result);
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580 sequence.setPDBfile(pdb);
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582 ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;
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583 ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;
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584 // ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();
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586 rotCanvas rc = new rotCanvas(pdb);
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587 JInternalFrame frame = new JInternalFrame();
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588 frame.setContentPane(rc);
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589 Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
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591 catch (Exception ex)
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593 ex.printStackTrace();
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597 protected void outline_actionPerformed(ActionEvent e)
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599 SequenceGroup sg = getGroup();
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600 Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);
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602 sg.setOutlineColour(col);
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