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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10 public class PopupMenu extends JPopupMenu
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12 JMenu groupMenu = new JMenu();
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13 JMenuItem copyGroup = new JMenuItem();
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14 JMenuItem moveGroup = new JMenuItem();
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15 JMenuItem deleteSequences = new JMenuItem();
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16 JMenuItem analyze = new JMenuItem();
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17 JMenu defineMenu = new JMenu();
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18 JMenuItem groupName = new JMenuItem();
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19 JMenuItem groupAnnotation = new JMenuItem();
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20 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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21 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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22 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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23 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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24 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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25 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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26 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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27 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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28 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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29 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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30 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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31 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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32 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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33 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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37 JMenu sequenceMenu = new JMenu();
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38 JMenuItem sequenceName = new JMenuItem();
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39 JMenu residueMenu = new JMenu();
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40 JMenuItem annotateResidue = new JMenuItem();
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43 JMenuItem unGroupMenuItem = new JMenuItem();
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45 public PopupMenu(AlignmentPanel ap, SequenceI seq)
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47 ///////////////////////////////////////////////////////////
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48 // If this is activated from the sequence panel, the user may want to
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49 // edit or annotate a particular residue. Therefore display the residue menu
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51 // If from the IDPanel, we must display the sequence menu
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52 //////////////////////////////////////////////////////////
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57 ButtonGroup colours = new ButtonGroup();
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58 colours.add(noColourmenuItem);
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59 colours.add(clustalColour);
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60 colours.add(zappoColour);
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61 colours.add(taylorColour);
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62 colours.add(hydrophobicityColour);
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63 colours.add(helixColour);
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64 colours.add(strandColour);
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65 colours.add(turnColour);
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66 colours.add(buriedColour);
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67 colours.add(abovePIDColour);
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68 colours.add(userDefinedColour);
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69 colours.add(PIDColour);
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70 colours.add(BLOSUM62Colour);
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75 { e.printStackTrace(); }
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77 SequenceGroup sg = ap.av.getRubberbandGroup();
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80 groupName.setText(sg.getName());
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81 if(sg.cs instanceof ZappoColourScheme)
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82 zappoColour.setSelected(true);
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83 else if(sg.cs instanceof TaylorColourScheme)
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84 taylorColour.setSelected(true);
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85 else if (sg.cs instanceof PIDColourScheme)
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86 PIDColour.setSelected(true);
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87 else if (sg.cs instanceof Blosum62ColourScheme)
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88 BLOSUM62Colour.setSelected(true);
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89 else if (sg.cs instanceof UserColourScheme)
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90 userDefinedColour.setSelected(true);
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91 else if (sg.cs instanceof HydrophobicColourScheme)
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92 hydrophobicityColour.setSelected(true);
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93 else if (sg.cs instanceof HelixColourScheme)
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94 helixColour.setSelected(true);
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95 else if (sg.cs instanceof StrandColourScheme)
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96 strandColour.setSelected(true);
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97 else if (sg.cs instanceof TurnColourScheme)
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98 turnColour.setSelected(true);
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99 else if (sg.cs instanceof BuriedColourScheme)
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100 buriedColour.setSelected(true);
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101 else if (sg.cs instanceof ClustalxColourScheme)
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102 clustalColour.setSelected(true);
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104 noColourmenuItem.setSelected(true);
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106 if (sg.cs instanceof ConservationColourScheme)
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107 conservationMenuItem.setSelected(true);
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113 residueMenu.setVisible(false);
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114 sequenceName.setText( sequence.getName() );
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117 sequenceMenu.setVisible(false);
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120 private void jbInit() throws Exception
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122 groupMenu.setText("Group");
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123 copyGroup.setText("Copy region to new Alignment");
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124 copyGroup.addActionListener(new java.awt.event.ActionListener()
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126 public void actionPerformed(ActionEvent e)
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128 copyGroup_actionPerformed(e);
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131 moveGroup.setText("Move sequences to new Alignment");
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132 moveGroup.addActionListener(new java.awt.event.ActionListener()
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134 public void actionPerformed(ActionEvent e)
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136 moveGroup_actionPerformed(e);
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139 deleteSequences.setText("Delete sequences");
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140 deleteSequences.addActionListener(new java.awt.event.ActionListener()
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142 public void actionPerformed(ActionEvent e)
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144 deleteSequences_actionPerformed(e);
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147 analyze.setText("Analyze");
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148 analyze.addActionListener(new java.awt.event.ActionListener()
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150 public void actionPerformed(ActionEvent e)
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152 analyze_actionPerformed(e);
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155 defineMenu.setText("Define");
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156 groupName.setText("Name");
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157 groupName.addActionListener(new java.awt.event.ActionListener()
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159 public void actionPerformed(ActionEvent e)
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161 groupName_actionPerformed(e);
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164 groupAnnotation.setText("Annotation");
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165 groupAnnotation.addActionListener(new java.awt.event.ActionListener()
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167 public void actionPerformed(ActionEvent e)
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169 groupAnnotation_actionPerformed(e);
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172 sequenceMenu.setText("Sequence");
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173 sequenceName.setText("sequenceName");
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174 sequenceName.addActionListener(new java.awt.event.ActionListener()
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176 public void actionPerformed(ActionEvent e)
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178 sequenceName_actionPerformed(e);
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181 residueMenu.setText("Residue");
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182 annotateResidue.setText("annotate residue???");
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183 PIDColour.setFocusPainted(false);
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184 unGroupMenuItem.setText("Remove Group");
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185 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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187 public void actionPerformed(ActionEvent e)
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189 unGroupMenuItem_actionPerformed(e);
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193 this.add(sequenceMenu);
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194 this.add(residueMenu);
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195 groupMenu.add(defineMenu);
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196 groupMenu.add(unGroupMenuItem);
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197 groupMenu.addSeparator();
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198 groupMenu.add(copyGroup);
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199 groupMenu.add(moveGroup);
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200 groupMenu.add(deleteSequences);
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201 groupMenu.addSeparator();
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202 groupMenu.add(analyze);
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203 defineMenu.add(groupName);
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204 defineMenu.add(groupAnnotation);
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205 defineMenu.addSeparator();
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206 defineMenu.add(noColourmenuItem);
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207 defineMenu.add(clustalColour);
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208 defineMenu.add(zappoColour);
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209 defineMenu.add(taylorColour);
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210 defineMenu.add(hydrophobicityColour);
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211 defineMenu.add(helixColour);
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212 defineMenu.add(strandColour);
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213 defineMenu.add(turnColour);
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214 defineMenu.add(buriedColour);
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215 defineMenu.add(userDefinedColour);
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216 defineMenu.add(PIDColour);
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217 defineMenu.add(BLOSUM62Colour);
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218 defineMenu.addSeparator();
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219 defineMenu.add(abovePIDColour);
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220 defineMenu.add(conservationMenuItem);
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222 sequenceMenu.add(sequenceName);
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223 residueMenu.add(annotateResidue);
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225 noColourmenuItem.setText("None");
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226 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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228 public void actionPerformed(ActionEvent e)
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230 noColourmenuItem_actionPerformed(e);
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234 clustalColour.setText("Clustalx colours");
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235 clustalColour.addActionListener(new java.awt.event.ActionListener()
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237 public void actionPerformed(ActionEvent e)
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239 clustalColour_actionPerformed(e);
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242 zappoColour.setText("Zappo colour scheme");
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243 zappoColour.addActionListener(new java.awt.event.ActionListener()
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245 public void actionPerformed(ActionEvent e)
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247 zappoColour_actionPerformed(e);
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250 taylorColour.setText("Taylor colour scheme");
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251 taylorColour.addActionListener(new java.awt.event.ActionListener()
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253 public void actionPerformed(ActionEvent e)
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255 taylorColour_actionPerformed(e);
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258 hydrophobicityColour.setText("By hydrophobicity");
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259 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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261 public void actionPerformed(ActionEvent e)
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263 hydrophobicityColour_actionPerformed(e);
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266 helixColour.setText("Helix propensity");
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267 helixColour.addActionListener(new java.awt.event.ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 helixColour_actionPerformed(e);
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274 strandColour.setText("Strand propensity");
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275 strandColour.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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279 strandColour_actionPerformed(e);
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282 turnColour.setText("Turn propensity");
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283 turnColour.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 turnColour_actionPerformed(e);
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290 buriedColour.setText("Buried index");
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291 buriedColour.addActionListener(new java.awt.event.ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 buriedColour_actionPerformed(e);
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298 abovePIDColour.setText("Above PID threshold only");
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299 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 abovePIDColour_actionPerformed(e);
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306 userDefinedColour.setText("User defined colours");
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307 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 userDefinedColour_actionPerformed(e);
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314 PIDColour.setText("Percentage Identity");
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315 PIDColour.addActionListener(new java.awt.event.ActionListener()
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317 public void actionPerformed(ActionEvent e)
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319 PIDColour_actionPerformed(e);
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322 BLOSUM62Colour.setText("BLOSUM62 score");
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323 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 BLOSUM62Colour_actionPerformed(e);
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330 conservationMenuItem.setText("By conservation");
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331 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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333 public void actionPerformed(ActionEvent e)
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335 conservationMenuItem_actionPerformed(e);
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345 SequenceGroup sg = getGroup();
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346 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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348 superG.setSuperGroupProperties( sg );
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350 ap.seqPanel.seqCanvas.paintFlag=true;
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351 ap.seqPanel.repaint();
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354 protected void clustalColour_actionPerformed(ActionEvent e)
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356 SequenceGroup sg = getGroup();
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357 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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361 protected void zappoColour_actionPerformed(ActionEvent e)
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363 getGroup().cs = new ZappoColourScheme();
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367 protected void taylorColour_actionPerformed(ActionEvent e)
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369 getGroup().cs = new TaylorColourScheme();
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374 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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376 getGroup().cs = new HydrophobicColourScheme();
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380 protected void helixColour_actionPerformed(ActionEvent e)
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382 getGroup().cs = new HelixColourScheme();
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386 protected void strandColour_actionPerformed(ActionEvent e)
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388 getGroup().cs = new StrandColourScheme();
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392 protected void turnColour_actionPerformed(ActionEvent e)
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394 getGroup().cs = new TurnColourScheme();
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398 protected void buriedColour_actionPerformed(ActionEvent e)
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400 getGroup().cs = new BuriedColourScheme();
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405 protected void abovePIDColour_actionPerformed(ActionEvent e)
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407 Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());
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411 protected void userDefinedColour_actionPerformed(ActionEvent e)
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413 JInternalFrame frame = new JInternalFrame();
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414 UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
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415 frame.setContentPane(chooser);
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416 Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
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417 frame.setResizable(false);
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418 frame.setIconifiable(false);
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419 frame.setMaximizable(false);
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423 protected void PIDColour_actionPerformed(ActionEvent e)
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428 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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430 getGroup().cs = new Blosum62ColourScheme(ap.av);
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435 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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437 getGroup().cs = null;
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441 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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443 SequenceGroup sg = getGroup();
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445 if(conservationMenuItem.isSelected())
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448 Conservation c = new Conservation("Group",
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449 ResidueProperties.propHash, 3,
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451 ap.av.alignment.getWidth());
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454 c.verdict(false, 100);
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455 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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460 Desktop.setConservationSliderSource(ap, ccs, sg.getName());
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462 else // remove ConservationColouring
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464 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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471 protected void groupAnnotation_actionPerformed(ActionEvent e)
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476 protected void groupName_actionPerformed(ActionEvent e)
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478 SequenceGroup sg = getGroup();
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479 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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484 groupName.setText(reply);
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487 protected void copyGroup_actionPerformed(ActionEvent e)
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489 SequenceGroup sg = ap.av.getRubberbandGroup();
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491 SequenceI[] s = new Sequence[sg.sequences.size()];
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492 for (int i=0; i < sg.sequences.size(); i++)
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494 s[i] = new Sequence( sg.getSequenceAt(i));
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495 s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
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497 AlignFrame af = new AlignFrame(new Alignment(s));
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498 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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499 if (newHeight > 500)
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501 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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504 protected void moveGroup_actionPerformed(ActionEvent e)
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506 SequenceGroup sg = ap.av.getRubberbandGroup();
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508 SequenceI[] s = new Sequence[sg.sequences.size()];
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510 for (int i=0; i < sg.sequences.size(); i++)
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511 s[i] = new Sequence( sg.getSequenceAt(i));
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513 AlignFrame af = new AlignFrame(new Alignment(s));
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514 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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517 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
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520 for (int i=0; i < sg.sequences.size(); i++)
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521 ap.av.alignment.deleteSequence(sg.getSequenceAt(i));
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524 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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525 ap.RefreshPanels();
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530 protected void deleteSequences_actionPerformed(ActionEvent e)
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532 SequenceGroup sg = ap.av.getRubberbandGroup();
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533 for (int i=0;i < sg.sequences.size(); i++)
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534 ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));
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536 ap.av.alignment.deleteGroup(sg);
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537 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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538 ap.RefreshPanels();
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542 protected void analyze_actionPerformed(ActionEvent e)
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544 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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545 JInternalFrame frame = new JInternalFrame();
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546 cap.formatForOutput();
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547 frame.setContentPane(cap);
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548 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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549 SequenceGroup sg = getGroup();
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550 StringBuffer sb = new StringBuffer();
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552 for(int i=0; i<sg.sequences.size(); i++)
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554 Sequence tmp = (Sequence)sg.sequences.get(i);
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555 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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559 sb.append("Something amazing will happen soon");
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560 cap.setText( sb.toString() );
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564 SequenceGroup getGroup()
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566 SequenceGroup sg = ap.av.getRubberbandGroup();
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568 // this method won't add a new group if it already exists
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569 ap.av.alignment.addGroup(sg);
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573 void sequenceName_actionPerformed(ActionEvent e)
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575 String id = sequence.getName();
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576 String s = (String)JOptionPane.showInternalInputDialog(
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578 "Edit sequence name",
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579 "Edit sequence name",
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580 JOptionPane.PLAIN_MESSAGE,
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587 sequence.setName(s);
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588 ap.RefreshPanels();
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593 void unGroupMenuItem_actionPerformed(ActionEvent e)
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595 SequenceGroup sg = ap.av.getRubberbandGroup();
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596 ap.av.alignment.deleteGroup(sg);
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597 ap.av.setRubberbandGroup(null);
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598 ap.RefreshPanels();
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