1 package jalview.appletgui;
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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 java.awt.event.*;
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9 public class APopupMenu extends java.awt.PopupMenu
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11 Menu groupMenu = new Menu();
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12 protected MenuItem clustalColour = new MenuItem();
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13 protected MenuItem zappoColour = new MenuItem();
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14 protected MenuItem taylorColour = new MenuItem();
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15 protected MenuItem hydrophobicityColour = new MenuItem();
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16 protected MenuItem helixColour = new MenuItem();
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17 protected MenuItem strandColour = new MenuItem();
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18 protected MenuItem turnColour = new MenuItem();
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19 protected MenuItem buriedColour = new MenuItem();
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20 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
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21 protected MenuItem userDefinedColour = new MenuItem();
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22 protected MenuItem PIDColour = new MenuItem();
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23 protected MenuItem BLOSUM62Colour = new MenuItem();
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24 MenuItem noColourmenuItem = new MenuItem();
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25 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
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29 Menu sequenceMenu = new Menu();
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30 MenuItem sequenceName = new MenuItem();
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32 MenuItem unGroupMenuItem = new MenuItem();
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33 MenuItem nucleotideMenuItem = new MenuItem();
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34 Menu colourMenu = new Menu();
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35 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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36 CheckboxMenuItem showText = new CheckboxMenuItem();
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37 CheckboxMenuItem showColourText = new CheckboxMenuItem();
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39 public APopupMenu(AlignmentPanel ap, Sequence seq)
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41 ///////////////////////////////////////////////////////////
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42 // If this is activated from the sequence panel, the user may want to
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43 // edit or annotate a particular residue. Therefore display the residue menu
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45 // If from the IDPanel, we must display the sequence menu
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46 //////////////////////////////////////////////////////////
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54 { e.printStackTrace(); }
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57 SequenceGroup sg = ap.av.getSelectionGroup();
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60 showText.setState(sg.getDisplayText());
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61 showColourText.setState(sg.getColourText());
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62 showBoxes.setState(sg.getDisplayBoxes());
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65 if( !ap.av.alignment.getGroups().contains(sg))
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66 groupMenu.remove(unGroupMenuItem);
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69 remove(sequenceMenu);
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73 private void jbInit() throws Exception
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75 groupMenu.setLabel("Group");
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76 groupMenu.setLabel("Define");
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78 sequenceMenu.setLabel("Sequence");
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79 sequenceName.setLabel("Edit name");
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80 unGroupMenuItem.setLabel("Remove Group");
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81 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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83 public void actionPerformed(ActionEvent e)
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85 unGroupMenuItem_actionPerformed(e);
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90 nucleotideMenuItem.setLabel("Nucleotide");
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91 nucleotideMenuItem.addActionListener(new ActionListener()
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93 public void actionPerformed(ActionEvent e)
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95 nucleotideMenuItem_actionPerformed(e);
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98 conservationMenuItem.addItemListener(new ItemListener()
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100 public void itemStateChanged(ItemEvent itemEvent)
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102 conservationMenuItem_itemStateChanged(itemEvent);
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105 abovePIDColour.addItemListener(new ItemListener()
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107 public void itemStateChanged(ItemEvent itemEvent)
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109 abovePIDColour_itemStateChanged(itemEvent);
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112 colourMenu.setLabel("Group Colour");
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113 showBoxes.setLabel("Boxes");
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114 showBoxes.setState(true);
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115 showBoxes.addItemListener(new ItemListener()
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117 public void itemStateChanged(ItemEvent itemEvent)
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119 showBoxes_itemStateChanged(itemEvent);
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123 showText.setLabel("Text");
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124 showText.addItemListener(new ItemListener()
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126 public void itemStateChanged(ItemEvent itemEvent)
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128 showText_itemStateChanged(itemEvent);
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131 showColourText.setLabel("Colour Text");
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132 showColourText.addItemListener(new ItemListener()
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134 public void itemStateChanged(ItemEvent itemEvent)
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136 showColourText_itemStateChanged(itemEvent);
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141 this.add(sequenceMenu);
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142 groupMenu.add(unGroupMenuItem);
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143 groupMenu.add(colourMenu);
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144 groupMenu.addSeparator();
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145 groupMenu.add(showBoxes);
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146 groupMenu.add(showText);
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147 groupMenu.add(showColourText);
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148 sequenceMenu.add(sequenceName);
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149 colourMenu.add(noColourmenuItem);
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150 colourMenu.add(clustalColour);
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151 colourMenu.add(BLOSUM62Colour);
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152 colourMenu.add(PIDColour);
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153 colourMenu.add(zappoColour);
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154 colourMenu.add(taylorColour);
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155 colourMenu.add(hydrophobicityColour);
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156 colourMenu.add(helixColour);
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157 colourMenu.add(strandColour);
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158 colourMenu.add(turnColour);
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159 colourMenu.add(buriedColour);
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160 colourMenu.add(nucleotideMenuItem);
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161 colourMenu.add(userDefinedColour);
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162 colourMenu.addSeparator();
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163 colourMenu.add(abovePIDColour);
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164 colourMenu.add(conservationMenuItem);
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166 noColourmenuItem.setLabel("None");
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167 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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169 public void actionPerformed(ActionEvent e)
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171 noColourmenuItem_actionPerformed(e);
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175 clustalColour.setLabel("Clustalx colours");
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176 clustalColour.addActionListener(new java.awt.event.ActionListener()
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178 public void actionPerformed(ActionEvent e)
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180 clustalColour_actionPerformed(e);
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183 zappoColour.setLabel("Zappo");
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184 zappoColour.addActionListener(new java.awt.event.ActionListener()
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186 public void actionPerformed(ActionEvent e)
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188 zappoColour_actionPerformed(e);
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191 taylorColour.setLabel("Taylor");
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192 taylorColour.addActionListener(new java.awt.event.ActionListener()
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194 public void actionPerformed(ActionEvent e)
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196 taylorColour_actionPerformed(e);
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199 hydrophobicityColour.setLabel("Hydrophobicity");
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200 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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202 public void actionPerformed(ActionEvent e)
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204 hydrophobicityColour_actionPerformed(e);
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207 helixColour.setLabel("Helix propensity");
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208 helixColour.addActionListener(new java.awt.event.ActionListener()
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210 public void actionPerformed(ActionEvent e)
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212 helixColour_actionPerformed(e);
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215 strandColour.setLabel("Strand propensity");
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216 strandColour.addActionListener(new java.awt.event.ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 strandColour_actionPerformed(e);
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223 turnColour.setLabel("Turn propensity");
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224 turnColour.addActionListener(new java.awt.event.ActionListener()
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226 public void actionPerformed(ActionEvent e)
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228 turnColour_actionPerformed(e);
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231 buriedColour.setLabel("Buried Index");
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232 buriedColour.addActionListener(new java.awt.event.ActionListener()
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234 public void actionPerformed(ActionEvent e)
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236 buriedColour_actionPerformed(e);
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239 abovePIDColour.setLabel("Above % Identity");
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241 userDefinedColour.setLabel("User Defined");
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242 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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244 public void actionPerformed(ActionEvent e)
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246 userDefinedColour_actionPerformed(e);
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249 PIDColour.setLabel("Percentage Identity");
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250 PIDColour.addActionListener(new java.awt.event.ActionListener()
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252 public void actionPerformed(ActionEvent e)
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254 PIDColour_actionPerformed(e);
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257 BLOSUM62Colour.setLabel("BLOSUM62");
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258 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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260 public void actionPerformed(ActionEvent e)
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262 BLOSUM62Colour_actionPerformed(e);
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265 conservationMenuItem.setLabel("Conservation");
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272 SequenceGroup sg = getGroup();
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273 SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
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275 superG.setSuperGroupProperties( sg );
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277 ap.seqPanel.seqCanvas.repaint();
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280 protected void clustalColour_actionPerformed(ActionEvent e)
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282 SequenceGroup sg = getGroup();
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283 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
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287 protected void zappoColour_actionPerformed(ActionEvent e)
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289 getGroup().cs = new ZappoColourScheme();
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293 protected void taylorColour_actionPerformed(ActionEvent e)
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295 getGroup().cs = new TaylorColourScheme();
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300 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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302 getGroup().cs = new HydrophobicColourScheme();
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306 protected void helixColour_actionPerformed(ActionEvent e)
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308 getGroup().cs = new HelixColourScheme();
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312 protected void strandColour_actionPerformed(ActionEvent e)
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314 getGroup().cs = new StrandColourScheme();
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318 protected void turnColour_actionPerformed(ActionEvent e)
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320 getGroup().cs = new TurnColourScheme();
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324 protected void buriedColour_actionPerformed(ActionEvent e)
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326 getGroup().cs = new BuriedColourScheme();
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330 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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332 getGroup().cs = new NucleotideColourScheme();
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338 protected void abovePIDColour_itemStateChanged(ItemEvent ie)
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340 SequenceGroup sg = getGroup();
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341 if (abovePIDColour.getState())
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343 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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344 ap.av.alignment.getWidth()));
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345 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
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346 if (sg.cs instanceof ResidueColourScheme)
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347 ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
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348 else if (sg.cs instanceof ScoreColourScheme)
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349 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
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351 SliderPanel.showPIDSlider();
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355 else // remove PIDColouring
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357 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
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358 rcs.setThreshold(0);
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367 protected void userDefinedColour_actionPerformed(ActionEvent e)
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369 new UserDefinedColours( ap, getGroup());
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372 protected void PIDColour_actionPerformed(ActionEvent e)
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374 SequenceGroup sg = getGroup();
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375 sg.cs = new PIDColourScheme();
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376 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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377 ap.av.alignment.getWidth()));
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381 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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383 SequenceGroup sg = getGroup();
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385 sg.cs = new Blosum62ColourScheme();
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387 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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388 ap.av.alignment.getWidth()));
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394 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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396 getGroup().cs = null;
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400 protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
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402 SequenceGroup sg = getGroup();
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404 if(conservationMenuItem.getState())
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407 Conservation c = new Conservation("Group",
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408 ResidueProperties.propHash, 3,
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410 ap.av.alignment.getWidth());
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413 c.verdict(false, ap.av.ConsPercGaps);
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414 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
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419 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
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420 SliderPanel.showConservationSlider();
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422 else // remove ConservationColouring
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424 ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
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432 protected void analyze_actionPerformed(ActionEvent e)
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434 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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435 Frame frame = new Frame();
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437 jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
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438 SequenceGroup sg = getGroup();
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439 StringBuffer sb = new StringBuffer();
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441 for(int i=0; i<sg.sequences.size(); i++)
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443 Sequence tmp = (Sequence)sg.sequences.elementAt(i);
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444 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
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448 sb.append("Something amazing will happen soon");
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449 cap.setText( sb.toString() );
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453 SequenceGroup getGroup()
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455 SequenceGroup sg = ap.av.getSelectionGroup();
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457 // this method won't add a new group if it already exists
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458 ap.av.alignment.addGroup(sg);
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463 void unGroupMenuItem_actionPerformed(ActionEvent e)
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465 SequenceGroup sg = ap.av.getSelectionGroup();
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466 ap.av.alignment.deleteGroup(sg);
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467 ap.av.setSelectionGroup(null);
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472 public void showColourText_itemStateChanged(ItemEvent itemEvent)
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474 getGroup().setColourText(showColourText.getState());
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478 public void showText_itemStateChanged(ItemEvent itemEvent)
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480 getGroup().setDisplayText(showText.getState());
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484 public void showBoxes_itemStateChanged(ItemEvent itemEvent)
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486 getGroup().setDisplayBoxes(showBoxes.getState());
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