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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44 public PopupMenu(AlignmentPanel ap, SequenceI seq)
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46 ///////////////////////////////////////////////////////////
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47 // If this is activated from the sequence panel, the user may want to
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48 // edit or annotate a particular residue. Therefore display the residue menu
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50 // If from the IDPanel, we must display the sequence menu
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51 //////////////////////////////////////////////////////////
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56 ButtonGroup colours = new ButtonGroup();
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57 colours.add(noColourmenuItem);
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58 colours.add(clustalColour);
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59 colours.add(zappoColour);
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60 colours.add(taylorColour);
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61 colours.add(hydrophobicityColour);
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62 colours.add(helixColour);
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63 colours.add(strandColour);
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64 colours.add(turnColour);
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65 colours.add(buriedColour);
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66 colours.add(abovePIDColour);
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67 colours.add(userDefinedColour);
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68 colours.add(PIDColour);
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69 colours.add(BLOSUM62Colour);
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74 { e.printStackTrace(); }
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76 SequenceGroup sg = ap.av.getRubberbandGroup();
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79 groupName.setText(sg.getName());
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80 if(sg.cs instanceof ZappoColourScheme)
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81 zappoColour.setSelected(true);
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82 else if(sg.cs instanceof TaylorColourScheme)
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83 taylorColour.setSelected(true);
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84 else if (sg.cs instanceof PIDColourScheme)
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85 PIDColour.setSelected(true);
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86 else if (sg.cs instanceof Blosum62ColourScheme)
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87 BLOSUM62Colour.setSelected(true);
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88 else if (sg.cs instanceof UserColourScheme)
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89 userDefinedColour.setSelected(true);
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90 else if (sg.cs instanceof HydrophobicColourScheme)
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91 hydrophobicityColour.setSelected(true);
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92 else if (sg.cs instanceof HelixColourScheme)
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93 helixColour.setSelected(true);
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94 else if (sg.cs instanceof StrandColourScheme)
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95 strandColour.setSelected(true);
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96 else if (sg.cs instanceof TurnColourScheme)
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97 turnColour.setSelected(true);
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98 else if (sg.cs instanceof BuriedColourScheme)
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99 buriedColour.setSelected(true);
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100 else if (sg.cs instanceof ClustalxColourScheme)
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101 clustalColour.setSelected(true);
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103 noColourmenuItem.setSelected(true);
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105 if (sg.cs instanceof ConservationColourScheme)
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106 conservationMenuItem.setSelected(true);
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112 residueMenu.setVisible(false);
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113 sequenceName.setText( sequence.getName() );
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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("sequenceName");
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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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184 this.add(sequenceMenu);
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185 this.add(residueMenu);
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186 groupMenu.add(defineMenu);
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187 groupMenu.addSeparator();
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188 groupMenu.add(copyGroup);
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189 groupMenu.add(moveGroup);
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190 groupMenu.add(deleteSequences);
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191 groupMenu.addSeparator();
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192 groupMenu.add(analyze);
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193 defineMenu.add(groupName);
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194 defineMenu.add(groupAnnotation);
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195 defineMenu.addSeparator();
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196 defineMenu.add(noColourmenuItem);
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197 defineMenu.add(clustalColour);
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198 defineMenu.add(zappoColour);
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199 defineMenu.add(taylorColour);
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200 defineMenu.add(hydrophobicityColour);
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201 defineMenu.add(helixColour);
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202 defineMenu.add(strandColour);
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203 defineMenu.add(turnColour);
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204 defineMenu.add(buriedColour);
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205 defineMenu.add(userDefinedColour);
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206 defineMenu.add(PIDColour);
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207 defineMenu.add(BLOSUM62Colour);
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208 defineMenu.addSeparator();
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209 defineMenu.add(abovePIDColour);
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210 defineMenu.add(conservationMenuItem);
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212 sequenceMenu.add(sequenceName);
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213 residueMenu.add(annotateResidue);
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215 noColourmenuItem.setText("None");
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216 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 noColourmenuItem_actionPerformed(e);
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224 clustalColour.setText("Clustalx colours");
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225 clustalColour.addActionListener(new java.awt.event.ActionListener()
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227 public void actionPerformed(ActionEvent e)
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229 clustalColour_actionPerformed(e);
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232 zappoColour.setText("Zappo colour scheme");
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233 zappoColour.addActionListener(new java.awt.event.ActionListener()
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235 public void actionPerformed(ActionEvent e)
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237 zappoColour_actionPerformed(e);
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240 taylorColour.setText("Taylor colour scheme");
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241 taylorColour.addActionListener(new java.awt.event.ActionListener()
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243 public void actionPerformed(ActionEvent e)
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245 taylorColour_actionPerformed(e);
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248 hydrophobicityColour.setText("By hydrophobicity");
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249 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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251 public void actionPerformed(ActionEvent e)
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253 hydrophobicityColour_actionPerformed(e);
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256 helixColour.setText("Helix propensity");
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257 helixColour.addActionListener(new java.awt.event.ActionListener()
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259 public void actionPerformed(ActionEvent e)
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261 helixColour_actionPerformed(e);
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264 strandColour.setText("Strand propensity");
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265 strandColour.addActionListener(new java.awt.event.ActionListener()
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267 public void actionPerformed(ActionEvent e)
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269 strandColour_actionPerformed(e);
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272 turnColour.setText("Turn propensity");
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273 turnColour.addActionListener(new java.awt.event.ActionListener()
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275 public void actionPerformed(ActionEvent e)
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277 turnColour_actionPerformed(e);
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280 buriedColour.setText("Buried index");
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281 buriedColour.addActionListener(new java.awt.event.ActionListener()
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283 public void actionPerformed(ActionEvent e)
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285 buriedColour_actionPerformed(e);
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288 abovePIDColour.setText("Above PID threshold only");
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289 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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291 public void actionPerformed(ActionEvent e)
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293 abovePIDColour_actionPerformed(e);
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296 userDefinedColour.setText("User defined colours");
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297 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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299 public void actionPerformed(ActionEvent e)
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301 userDefinedColour_actionPerformed(e);
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304 PIDColour.setText("Percentage Identity");
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305 PIDColour.addActionListener(new java.awt.event.ActionListener()
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307 public void actionPerformed(ActionEvent e)
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309 PIDColour_actionPerformed(e);
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312 BLOSUM62Colour.setText("BLOSUM62 score");
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313 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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315 public void actionPerformed(ActionEvent e)
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317 BLOSUM62Colour_actionPerformed(e);
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320 conservationMenuItem.setText("By conservation");
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321 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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323 public void actionPerformed(ActionEvent e)
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325 conservationMenuItem_actionPerformed(e);
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335 ap.seqPanel.seqCanvas.paintFlag=true;
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336 ap.seqPanel.repaint();
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339 protected void clustalColour_actionPerformed(ActionEvent e)
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341 getGroup().cs = new ClustalxColourScheme();
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345 protected void zappoColour_actionPerformed(ActionEvent e)
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347 getGroup().cs = new ZappoColourScheme();
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351 protected void taylorColour_actionPerformed(ActionEvent e)
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353 getGroup().cs = new TaylorColourScheme();
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358 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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360 getGroup().cs = new HydrophobicColourScheme();
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364 protected void helixColour_actionPerformed(ActionEvent e)
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366 getGroup().cs = new HelixColourScheme();
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370 protected void strandColour_actionPerformed(ActionEvent e)
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372 getGroup().cs = new StrandColourScheme();
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376 protected void turnColour_actionPerformed(ActionEvent e)
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378 getGroup().cs = new TurnColourScheme();
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382 protected void buriedColour_actionPerformed(ActionEvent e)
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384 getGroup().cs = new BuriedColourScheme();
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390 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
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392 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
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393 JInternalFrame frame = new JInternalFrame();
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394 frame.setContentPane(cip);
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395 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
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396 frame.setMaximizable(false);
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401 protected void abovePIDColour_actionPerformed(ActionEvent e)
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403 SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );
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404 JInternalFrame frame = new JInternalFrame();
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405 frame.setContentPane(sp);
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406 Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);
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407 frame.setMaximizable(false);
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412 protected void userDefinedColour_actionPerformed(ActionEvent e)
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414 JInternalFrame frame = new JInternalFrame();
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415 UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
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416 frame.setContentPane(chooser);
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417 Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
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418 frame.setResizable(false);
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419 frame.setIconifiable(false);
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420 frame.setMaximizable(false);
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424 protected void PIDColour_actionPerformed(ActionEvent e)
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429 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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431 getGroup().cs = new Blosum62ColourScheme(ap.av);
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436 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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438 getGroup().cs = null;
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442 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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444 SequenceGroup sg = getGroup();
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446 Conservation c = new Conservation("Group",
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447 ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),
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451 c.verdict(false, 100);
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452 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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460 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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462 viewport.setGlobalColourScheme( null );
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467 public void clustalColour_actionPerformed(ActionEvent e)
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469 viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
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470 conservationMenuItem.setSelected(false);
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471 abovePIDThreshold.setSelected(false);
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475 public void zappoColour_actionPerformed(ActionEvent e)
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477 viewport.setGlobalColourScheme(new ZappoColourScheme() );
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481 public void taylorColour_actionPerformed(ActionEvent e)
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483 viewport.setGlobalColourScheme(new TaylorColourScheme() );
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488 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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490 viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
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494 public void helixColour_actionPerformed(ActionEvent e)
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496 viewport.setGlobalColourScheme( new HelixColourScheme() );
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501 public void strandColour_actionPerformed(ActionEvent e)
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503 viewport.setGlobalColourScheme(new StrandColourScheme() );
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508 public void turnColour_actionPerformed(ActionEvent e)
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510 viewport.setGlobalColourScheme(new TurnColourScheme() );
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515 public void buriedColour_actionPerformed(ActionEvent e)
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517 viewport.setGlobalColourScheme( new BuriedColourScheme() );
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521 void changeColour()
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523 if(abovePIDThreshold.isSelected())
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524 abovePIDThreshold_actionPerformed(null);
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525 else if(conservationMenuItem.isSelected())
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526 conservationMenuItem_actionPerformed(null);
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528 alignPanel.seqPanel.seqCanvas.paintFlag = true;
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529 alignPanel.repaint();
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532 void addConservationOrPIDColour()
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534 int x=0, y=0, threshold = 70;
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536 if(sliderFrame!=null)
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539 x = sliderFrame.getX();
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540 y = sliderFrame.getY();
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541 SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();
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542 threshold = sp.getValue();
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543 sliderFrame.setClosed(true);
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545 catch (Exception ex)
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546 { ex.printStackTrace(); }
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548 ColourSchemeI oldCs = viewport.getGlobalColourScheme();
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550 ConservationColourScheme ccs = null;
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551 if (oldCs instanceof ConservationColourScheme)
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552 ccs = (ConservationColourScheme) oldCs;
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554 if(conservationMenuItem.isSelected())
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556 Alignment al = (Alignment)viewport.alignment;
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557 Conservation c = new Conservation("All",
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558 ResidueProperties.propHash, 3, al.getSequences(), 0,
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562 c.verdict(false, 100);
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565 ccs = new ConservationColourScheme(c, ccs.cs);
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567 ccs = new ConservationColourScheme(c, oldCs);
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569 viewport.setGlobalColourScheme( ccs );
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572 else if(oldCs instanceof ConservationColourScheme)
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575 viewport.setGlobalColourScheme( oldCs );
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579 if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )
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581 sliderFrame = new JInternalFrame();
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582 sliderFrame.setMaximizable(false);
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583 sliderFrame.setResizable(false);
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585 SliderPanel sp = null;
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586 if (conservationMenuItem.isSelected())
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590 sp = new SliderPanel(alignPanel, threshold, true,ccs);
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591 Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90);
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594 else if (abovePIDThreshold.isSelected())
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596 sp = new SliderPanel(alignPanel, threshold, false, oldCs);
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598 Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);
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601 sliderFrame.setContentPane(sp);
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603 sliderFrame.setLocation(x,y);
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610 if (oldCs instanceof ResidueColourScheme)
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612 ResidueColourScheme rcs = (ResidueColourScheme) oldCs;
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613 rcs.setThreshold(threshold);
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615 else if (oldCs instanceof ScoreColourScheme)
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617 ScoreColourScheme scs = (ScoreColourScheme) oldCs;
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618 scs.setThreshold(threshold);
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621 alignPanel.seqPanel.seqCanvas.paintFlag = true;
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622 alignPanel.repaint();
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626 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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628 if(abovePIDThreshold.isSelected())
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629 abovePIDThreshold.setSelected(false);
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631 viewport.setConservationSelected(conservationMenuItem.isSelected());
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633 addConservationOrPIDColour();
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636 JInternalFrame sliderFrame;
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637 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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639 if(conservationMenuItem.isSelected())
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640 conservationMenuItem.setSelected(false);
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642 addConservationOrPIDColour();
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647 public void userDefinedColour_actionPerformed(ActionEvent e)
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649 JInternalFrame frame = new JInternalFrame();
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650 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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651 frame.setContentPane(chooser);
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652 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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653 frame.setResizable(false);
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654 frame.setIconifiable(false);
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655 frame.setMaximizable(false);
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658 public void PIDColour_actionPerformed(ActionEvent e)
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660 viewport.setGlobalColourScheme( new PIDColourScheme() );
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661 alignPanel.setColourScheme( );
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665 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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667 viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );
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668 alignPanel.setColourScheme();
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671 //////////////////////////////////////
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672 protected void groupAnnotation_actionPerformed(ActionEvent e)
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677 protected void groupName_actionPerformed(ActionEvent e)
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679 SequenceGroup sg = getGroup();
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680 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
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685 groupName.setText(reply);
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688 protected void copyGroup_actionPerformed(ActionEvent e)
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690 SequenceGroup sg = ap.av.getRubberbandGroup();
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692 SequenceI[] s = new Sequence[sg.sequences.size()];
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693 for (int i=0; i < sg.sequences.size(); i++)
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695 s[i] = new Sequence( sg.getSequenceAt(i));
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696 s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
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698 AlignFrame af = new AlignFrame(new Alignment(s));
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699 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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700 if (newHeight > 500)
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702 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
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705 protected void moveGroup_actionPerformed(ActionEvent e)
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707 SequenceGroup sg = ap.av.getRubberbandGroup();
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709 SequenceI[] s = new Sequence[sg.sequences.size()];
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711 for (int i=0; i < sg.sequences.size(); i++)
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712 s[i] = new Sequence( sg.getSequenceAt(i));
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714 AlignFrame af = new AlignFrame(new Alignment(s));
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715 int newHeight = s.length * af.viewport.getCharHeight() + 200;
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718 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
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721 for (int i=0; i < sg.sequences.size(); i++)
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722 ap.av.alignment.deleteSequence(sg.getSequenceAt(i));
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725 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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726 ap.RefreshPanels();
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731 protected void deleteSequences_actionPerformed(ActionEvent e)
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733 SequenceGroup sg = ap.av.getRubberbandGroup();
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734 for (int i=0;i < sg.sequences.size(); i++)
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735 ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));
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737 ap.av.alignment.deleteGroup(sg);
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738 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
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739 ap.seqPanel.parent.RefreshPanels();
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743 protected void analyze_actionPerformed(ActionEvent e)
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745 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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746 JInternalFrame frame = new JInternalFrame();
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747 cap.formatForOutput();
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748 frame.setContentPane(cap);
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749 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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750 SequenceGroup sg = getGroup();
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751 StringBuffer sb = new StringBuffer();
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753 for(int i=0; i<sg.sequences.size(); i++)
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755 Sequence tmp = (Sequence)sg.sequences.get(i);
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756 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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760 sb.append("Something amazing will happen soon");
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761 cap.setText( sb.toString() );
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765 SequenceGroup getGroup()
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767 SequenceGroup sg = ap.av.getRubberbandGroup();
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769 // this method won't add a new group if it already exists
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770 ap.av.alignment.addGroup(sg);
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774 void sequenceName_actionPerformed(ActionEvent e)
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776 String id = sequence.getName();
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777 String s = (String)JOptionPane.showInternalInputDialog(
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779 "Edit sequence name",
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780 "Edit sequence name",
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781 JOptionPane.PLAIN_MESSAGE,
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788 sequence.setName(s);
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789 ap.RefreshPanels();
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