2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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23 import jalview.analysis.*;
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25 import jalview.datamodel.*;
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28 import jalview.schemes.*;
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31 import java.awt.event.*;
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33 import javax.swing.*;
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35 import java.util.Vector;
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42 * @version $Revision$
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44 public class PopupMenu extends JPopupMenu
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46 JMenu groupMenu = new JMenu();
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47 JMenuItem groupName = new JMenuItem();
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48 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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49 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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56 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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57 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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60 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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61 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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63 JMenu sequenceMenu = new JMenu();
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64 JMenuItem sequenceName = new JMenuItem();
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66 JMenuItem unGroupMenuItem = new JMenuItem();
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67 JMenuItem outline = new JMenuItem();
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68 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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69 JMenu colourMenu = new JMenu();
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70 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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71 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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72 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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73 JMenu editMenu = new JMenu();
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74 JMenuItem cut = new JMenuItem();
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75 JMenuItem copy = new JMenuItem();
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76 JMenuItem upperCase = new JMenuItem();
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77 JMenuItem lowerCase = new JMenuItem();
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78 JMenuItem toggle = new JMenuItem();
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81 * Creates a new PopupMenu object.
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83 * @param ap DOCUMENT ME!
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84 * @param seq DOCUMENT ME!
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86 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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88 ///////////////////////////////////////////////////////////
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89 // If this is activated from the sequence panel, the user may want to
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90 // edit or annotate a particular residue. Therefore display the residue menu
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92 // If from the IDPanel, we must display the sequence menu
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93 //////////////////////////////////////////////////////////
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97 ButtonGroup colours = new ButtonGroup();
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98 colours.add(noColourmenuItem);
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99 colours.add(clustalColour);
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100 colours.add(zappoColour);
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101 colours.add(taylorColour);
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102 colours.add(hydrophobicityColour);
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103 colours.add(helixColour);
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104 colours.add(strandColour);
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105 colours.add(turnColour);
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106 colours.add(buriedColour);
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107 colours.add(abovePIDColour);
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108 colours.add(userDefinedColour);
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109 colours.add(PIDColour);
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110 colours.add(BLOSUM62Colour);
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116 catch (Exception e)
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118 e.printStackTrace();
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124 JMenuItem menuItem;
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125 if( seq.getDatasetSequence().getPDBId() != null)
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127 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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129 while (e.hasMoreElements())
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131 final PDBEntry pdb = (PDBEntry) e.nextElement();
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133 menuItem = new JMenuItem();
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134 menuItem.setText("View PDB entry: " + pdb.getId());
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135 menuItem.addActionListener(new java.awt.event.ActionListener()
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137 public void actionPerformed(ActionEvent e)
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139 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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142 sequenceMenu.add(menuItem);
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146 /* menuItem = new JMenuItem("Hide Sequences");
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147 menuItem.addActionListener(new java.awt.event.ActionListener()
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149 public void actionPerformed(ActionEvent e)
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151 hideSequences(false);
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154 sequenceMenu.add(menuItem);
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156 if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)
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158 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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159 menuItem.addActionListener(new java.awt.event.ActionListener()
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161 public void actionPerformed(ActionEvent e)
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163 hideSequences(true);
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166 sequenceMenu.add(menuItem);
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174 SequenceGroup sg = ap.av.getSelectionGroup();
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178 groupName.setText(sg.getName());
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180 if (sg.cs instanceof ZappoColourScheme)
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182 zappoColour.setSelected(true);
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184 else if (sg.cs instanceof TaylorColourScheme)
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186 taylorColour.setSelected(true);
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188 else if (sg.cs instanceof PIDColourScheme)
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190 PIDColour.setSelected(true);
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192 else if (sg.cs instanceof Blosum62ColourScheme)
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194 BLOSUM62Colour.setSelected(true);
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196 else if (sg.cs instanceof UserColourScheme)
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198 userDefinedColour.setSelected(true);
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200 else if (sg.cs instanceof HydrophobicColourScheme)
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202 hydrophobicityColour.setSelected(true);
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204 else if (sg.cs instanceof HelixColourScheme)
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206 helixColour.setSelected(true);
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208 else if (sg.cs instanceof StrandColourScheme)
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210 strandColour.setSelected(true);
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212 else if (sg.cs instanceof TurnColourScheme)
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214 turnColour.setSelected(true);
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216 else if (sg.cs instanceof BuriedColourScheme)
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218 buriedColour.setSelected(true);
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220 else if (sg.cs instanceof ClustalxColourScheme)
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222 clustalColour.setSelected(true);
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226 noColourmenuItem.setSelected(true);
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229 if (sg.cs!=null && sg.cs.conservationApplied())
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231 conservationMenuItem.setSelected(true);
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234 showText.setSelected(sg.getDisplayText());
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235 showColourText.setSelected(sg.getColourText());
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236 showBoxes.setSelected(sg.getDisplayBoxes());
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240 groupMenu.setVisible(false);
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241 editMenu.setVisible(false);
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244 if (!ap.av.alignment.getGroups().contains(sg))
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246 unGroupMenuItem.setVisible(false);
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250 groupMenu.insertSeparator(3);
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255 sequenceMenu.setVisible(false);
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258 if(links != null && links.size()>0)
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260 JMenu linkMenu = new JMenu("Link");
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262 for(int i=0; i<links.size(); i++)
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264 String link = links.elementAt(i).toString();
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265 final String label = link.substring(0, link.indexOf("|"));
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266 item = new JMenuItem(label);
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269 if (link.indexOf("$SEQUENCE_ID$") > -1)
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271 String id = seq.getName();
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272 if (id.indexOf("|") > -1)
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273 id = id.substring(id.lastIndexOf("|") + 1);
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275 url = link.substring(link.indexOf("|") + 1,
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276 link.indexOf("$SEQUENCE_ID$"))
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278 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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281 url = link.substring(link.lastIndexOf("|")+1);
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284 item.addActionListener(new java.awt.event.ActionListener()
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286 public void actionPerformed(ActionEvent e)
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292 linkMenu.add(item);
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302 * @throws Exception DOCUMENT ME!
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304 private void jbInit() throws Exception
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306 groupMenu.setText("Group");
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307 groupMenu.setText("Group");
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308 groupName.setText("Name");
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309 groupName.addActionListener(new java.awt.event.ActionListener()
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311 public void actionPerformed(ActionEvent e)
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313 groupName_actionPerformed(e);
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316 sequenceMenu.setText("Sequence");
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317 sequenceName.setText("Edit Name/Description");
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318 sequenceName.addActionListener(new java.awt.event.ActionListener()
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320 public void actionPerformed(ActionEvent e)
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322 sequenceName_actionPerformed(e);
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325 PIDColour.setFocusPainted(false);
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326 unGroupMenuItem.setText("Remove Group");
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327 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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329 public void actionPerformed(ActionEvent e)
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331 unGroupMenuItem_actionPerformed(e);
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335 outline.setText("Border colour");
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336 outline.addActionListener(new java.awt.event.ActionListener()
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338 public void actionPerformed(ActionEvent e)
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340 outline_actionPerformed(e);
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343 nucleotideMenuItem.setText("Nucleotide");
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344 nucleotideMenuItem.addActionListener(new ActionListener()
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346 public void actionPerformed(ActionEvent e)
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348 nucleotideMenuItem_actionPerformed(e);
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351 colourMenu.setText("Group Colour");
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352 showBoxes.setText("Boxes");
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353 showBoxes.setState(true);
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354 showBoxes.addActionListener(new ActionListener()
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356 public void actionPerformed(ActionEvent e)
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358 showBoxes_actionPerformed(e);
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361 showText.setText("Text");
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362 showText.setState(true);
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363 showText.addActionListener(new ActionListener()
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365 public void actionPerformed(ActionEvent e)
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367 showText_actionPerformed(e);
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370 showColourText.setText("Colour Text");
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371 showColourText.addActionListener(new ActionListener()
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373 public void actionPerformed(ActionEvent e)
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375 showColourText_actionPerformed(e);
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378 editMenu.setText("Edit");
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379 cut.setText("Cut");
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380 cut.addActionListener(new ActionListener()
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382 public void actionPerformed(ActionEvent e)
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384 cut_actionPerformed(e);
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387 upperCase.setText("To Upper Case");
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388 upperCase.addActionListener(new ActionListener()
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390 public void actionPerformed(ActionEvent e)
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392 upperCase_actionPerformed(e);
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395 copy.setText("Copy");
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396 copy.addActionListener(new ActionListener()
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398 public void actionPerformed(ActionEvent e)
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400 copy_actionPerformed(e);
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403 lowerCase.setText("To Lower Case");
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404 lowerCase.addActionListener(new ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 lowerCase_actionPerformed(e);
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411 toggle.setText("Toggle Case");
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412 toggle.addActionListener(new ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 toggle_actionPerformed(e);
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421 this.add(editMenu);
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422 groupMenu.add(groupName);
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423 groupMenu.addSeparator();
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424 groupMenu.add(unGroupMenuItem);
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425 groupMenu.add(colourMenu);
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426 groupMenu.addSeparator();
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427 groupMenu.add(showBoxes);
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428 groupMenu.add(showText);
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429 groupMenu.add(showColourText);
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430 groupMenu.addSeparator();
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431 groupMenu.add(outline);
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432 sequenceMenu.add(sequenceName);
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433 colourMenu.add(noColourmenuItem);
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434 colourMenu.add(clustalColour);
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435 colourMenu.add(BLOSUM62Colour);
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436 colourMenu.add(PIDColour);
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437 colourMenu.add(zappoColour);
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438 colourMenu.add(taylorColour);
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439 colourMenu.add(hydrophobicityColour);
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440 colourMenu.add(helixColour);
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441 colourMenu.add(strandColour);
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442 colourMenu.add(turnColour);
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443 colourMenu.add(buriedColour);
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444 colourMenu.add(nucleotideMenuItem);
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445 colourMenu.add(userDefinedColour);
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447 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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449 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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450 getUserColourSchemes().keys();
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452 while (userColours.hasMoreElements())
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454 JMenuItem item = new JMenuItem(userColours.
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455 nextElement().toString());
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456 item.addActionListener(new ActionListener()
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458 public void actionPerformed(ActionEvent evt)
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460 userDefinedColour_actionPerformed(evt);
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463 colourMenu.add(item);
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468 colourMenu.addSeparator();
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469 colourMenu.add(abovePIDColour);
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470 colourMenu.add(conservationMenuItem);
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471 editMenu.add(copy);
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473 editMenu.add(upperCase);
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474 editMenu.add(lowerCase);
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475 editMenu.add(toggle);
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476 noColourmenuItem.setText("None");
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477 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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479 public void actionPerformed(ActionEvent e)
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481 noColourmenuItem_actionPerformed(e);
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485 clustalColour.setText("Clustalx colours");
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486 clustalColour.addActionListener(new java.awt.event.ActionListener()
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488 public void actionPerformed(ActionEvent e)
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490 clustalColour_actionPerformed(e);
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493 zappoColour.setText("Zappo");
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494 zappoColour.addActionListener(new java.awt.event.ActionListener()
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496 public void actionPerformed(ActionEvent e)
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498 zappoColour_actionPerformed(e);
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501 taylorColour.setText("Taylor");
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502 taylorColour.addActionListener(new java.awt.event.ActionListener()
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504 public void actionPerformed(ActionEvent e)
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506 taylorColour_actionPerformed(e);
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509 hydrophobicityColour.setText("Hydrophobicity");
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510 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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512 public void actionPerformed(ActionEvent e)
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514 hydrophobicityColour_actionPerformed(e);
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517 helixColour.setText("Helix propensity");
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518 helixColour.addActionListener(new java.awt.event.ActionListener()
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520 public void actionPerformed(ActionEvent e)
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522 helixColour_actionPerformed(e);
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525 strandColour.setText("Strand propensity");
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526 strandColour.addActionListener(new java.awt.event.ActionListener()
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528 public void actionPerformed(ActionEvent e)
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530 strandColour_actionPerformed(e);
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533 turnColour.setText("Turn propensity");
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534 turnColour.addActionListener(new java.awt.event.ActionListener()
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536 public void actionPerformed(ActionEvent e)
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538 turnColour_actionPerformed(e);
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541 buriedColour.setText("Buried Index");
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542 buriedColour.addActionListener(new java.awt.event.ActionListener()
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544 public void actionPerformed(ActionEvent e)
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546 buriedColour_actionPerformed(e);
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549 abovePIDColour.setText("Above % Identity");
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550 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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552 public void actionPerformed(ActionEvent e)
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554 abovePIDColour_actionPerformed(e);
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557 userDefinedColour.setText("User Defined...");
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558 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 userDefinedColour_actionPerformed(e);
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565 PIDColour.setText("Percentage Identity");
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566 PIDColour.addActionListener(new java.awt.event.ActionListener()
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568 public void actionPerformed(ActionEvent e)
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570 PIDColour_actionPerformed(e);
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573 BLOSUM62Colour.setText("BLOSUM62");
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574 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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576 public void actionPerformed(ActionEvent e)
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578 BLOSUM62Colour_actionPerformed(e);
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581 conservationMenuItem.setText("Conservation");
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582 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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584 public void actionPerformed(ActionEvent e)
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586 conservationMenuItem_actionPerformed(e);
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596 if (ap.overviewPanel != null)
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597 ap.overviewPanel.updateOverviewImage();
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599 ap.seqPanel.repaint();
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605 * @param e DOCUMENT ME!
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607 protected void clustalColour_actionPerformed(ActionEvent e)
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609 SequenceGroup sg = getGroup();
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610 sg.cs = new ClustalxColourScheme(sg.sequences,
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611 ap.av.alignment.getWidth());
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618 * @param e DOCUMENT ME!
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620 protected void zappoColour_actionPerformed(ActionEvent e)
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622 getGroup().cs = new ZappoColourScheme();
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629 * @param e DOCUMENT ME!
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631 protected void taylorColour_actionPerformed(ActionEvent e)
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633 getGroup().cs = new TaylorColourScheme();
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640 * @param e DOCUMENT ME!
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642 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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644 getGroup().cs = new HydrophobicColourScheme();
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651 * @param e DOCUMENT ME!
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653 protected void helixColour_actionPerformed(ActionEvent e)
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655 getGroup().cs = new HelixColourScheme();
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662 * @param e DOCUMENT ME!
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664 protected void strandColour_actionPerformed(ActionEvent e)
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666 getGroup().cs = new StrandColourScheme();
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673 * @param e DOCUMENT ME!
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675 protected void turnColour_actionPerformed(ActionEvent e)
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677 getGroup().cs = new TurnColourScheme();
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684 * @param e DOCUMENT ME!
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686 protected void buriedColour_actionPerformed(ActionEvent e)
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688 getGroup().cs = new BuriedColourScheme();
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695 * @param e DOCUMENT ME!
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697 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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699 getGroup().cs = new NucleotideColourScheme();
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706 * @param e DOCUMENT ME!
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708 protected void abovePIDColour_actionPerformed(ActionEvent e)
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710 SequenceGroup sg = getGroup();
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714 if (abovePIDColour.isSelected())
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716 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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717 ap.av.alignment.getWidth()));
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719 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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720 getGroup().getName());
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722 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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724 SliderPanel.showPIDSlider();
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726 else // remove PIDColouring
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728 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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737 * @param e DOCUMENT ME!
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739 protected void userDefinedColour_actionPerformed(ActionEvent e)
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741 SequenceGroup sg = getGroup();
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743 if (e.getActionCommand().equals("User Defined..."))
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744 new UserDefinedColours(ap, sg);
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747 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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748 getUserColourSchemes().get(e.getActionCommand());
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756 * @param e DOCUMENT ME!
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758 protected void PIDColour_actionPerformed(ActionEvent e)
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760 SequenceGroup sg = getGroup();
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761 sg.cs = new PIDColourScheme();
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762 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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763 ap.av.alignment.getWidth()));
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770 * @param e DOCUMENT ME!
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772 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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774 SequenceGroup sg = getGroup();
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776 sg.cs = new Blosum62ColourScheme();
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778 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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779 ap.av.alignment.getWidth()));
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787 * @param e DOCUMENT ME!
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789 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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791 getGroup().cs = null;
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798 * @param e DOCUMENT ME!
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800 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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802 SequenceGroup sg = getGroup();
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806 if (conservationMenuItem.isSelected())
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808 Conservation c = new Conservation("Group",
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809 ResidueProperties.propHash, 3, sg.sequences, 0,
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810 ap.av.alignment.getWidth());
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813 c.verdict(false, ap.av.ConsPercGaps);
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815 sg.cs.setConservation(c);
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817 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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818 SliderPanel.showConservationSlider();
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820 else // remove ConservationColouring
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822 sg.cs.setConservation(null);
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831 * @param e DOCUMENT ME!
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833 protected void groupName_actionPerformed(ActionEvent e)
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835 SequenceGroup sg = getGroup();
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836 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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837 "Enter new group name", "Edit group name",
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838 JOptionPane.QUESTION_MESSAGE);
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846 groupName.setText(reply);
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852 * @param e DOCUMENT ME!
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854 protected void analyze_actionPerformed(ActionEvent e)
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856 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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857 JInternalFrame frame = new JInternalFrame();
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858 frame.setContentPane(cap);
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859 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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861 SequenceGroup sg = getGroup();
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862 StringBuffer sb = new StringBuffer();
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864 for (int i = 0; i < sg.sequences.size(); i++)
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866 Sequence tmp = (Sequence) sg.sequences.get(i);
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867 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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871 sb.append("Something amazing will happen soon");
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872 cap.setText(sb.toString());
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878 * @return DOCUMENT ME!
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880 SequenceGroup getGroup()
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882 SequenceGroup sg = ap.av.getSelectionGroup();
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883 // this method won't add a new group if it already exists
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885 ap.av.alignment.addGroup(sg);
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893 * @param e DOCUMENT ME!
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895 void sequenceName_actionPerformed(ActionEvent e)
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897 JLabel idlabel = new JLabel( " Sequence Name ");
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898 JLabel desclabel = new JLabel("Sequence Description ");
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899 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
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900 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
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901 JTextField id = new JTextField(sequence.getName(), 40);
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902 JTextField description = new JTextField(sequence.getDescription(), 40);
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903 JPanel panel = new JPanel(new BorderLayout());
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904 JPanel panel2 = new JPanel(new BorderLayout());
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905 panel2.add(idlabel, BorderLayout.WEST);
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906 panel2.add(id, BorderLayout.CENTER);
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907 panel.add(panel2, BorderLayout.NORTH);
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908 panel2 = new JPanel(new BorderLayout());
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909 panel2.add(desclabel, BorderLayout.WEST);
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910 panel2.add(description, BorderLayout.CENTER);
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911 panel.add(panel2, BorderLayout.SOUTH);
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914 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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915 panel, "Edit Sequence Name/Description",
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916 JOptionPane.OK_CANCEL_OPTION );
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919 if (reply != JOptionPane.OK_OPTION )
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924 String s = id.getText();
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928 if (s.indexOf(" ") > -1)
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930 JOptionPane.showMessageDialog(ap,
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931 "Spaces have been converted to \"_\"",
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932 "No spaces allowed in Sequence Name",
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933 JOptionPane.WARNING_MESSAGE);
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936 s = s.replace(' ', '_');
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937 sequence.getDatasetSequence().setName(s);
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938 sequence.setName(s);
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942 sequence.getDatasetSequence().setDescription(description.getText());
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943 sequence.setDescription(description.getText());
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949 * @param e DOCUMENT ME!
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951 void unGroupMenuItem_actionPerformed(ActionEvent e)
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953 SequenceGroup sg = ap.av.getSelectionGroup();
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954 ap.av.alignment.deleteGroup(sg);
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955 ap.av.setSelectionGroup(null);
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963 * @param e DOCUMENT ME!
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965 protected void outline_actionPerformed(ActionEvent e)
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967 SequenceGroup sg = getGroup();
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968 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
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973 sg.setOutlineColour(col);
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982 * @param e DOCUMENT ME!
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984 public void showBoxes_actionPerformed(ActionEvent e)
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986 getGroup().setDisplayBoxes(showBoxes.isSelected());
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993 * @param e DOCUMENT ME!
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995 public void showText_actionPerformed(ActionEvent e)
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997 getGroup().setDisplayText(showText.isSelected());
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1004 * @param e DOCUMENT ME!
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1006 public void showColourText_actionPerformed(ActionEvent e)
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1008 getGroup().setColourText(showColourText.isSelected());
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1012 public void showLink(String url)
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1016 jalview.util.BrowserLauncher.openURL(url);
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1018 catch (Exception ex)
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1020 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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1021 "Unixers: Couldn't find default web browser."
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1022 +"\nAdd the full path to your browser in Preferences.",
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1023 "Web browser not found", JOptionPane.WARNING_MESSAGE );
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1026 ex.printStackTrace();
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1030 void hideSequences(boolean representGroup)
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1032 SequenceGroup sg = ap.av.getSelectionGroup();
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1033 if(sg==null || sg.getSize()<1)
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1035 ap.av.hideSequence(sequence);
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1040 while(index < sg.sequences.size())
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1042 if(representGroup && sg.getSequenceAt(index)!=sequence)
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1044 sequence.addHiddenSequence(sg.getSequenceAt(index));
\r
1045 ap.av.hideSequence(sg.getSequenceAt(index));
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1047 else if(!representGroup)
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1049 ap.av.hideSequence(sg.getSequenceAt(index));
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1054 ap.av.setSelectionGroup(null);
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1058 public void copy_actionPerformed(ActionEvent e)
\r
1060 ap.alignFrame.copy_actionPerformed(null);
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1063 public void cut_actionPerformed(ActionEvent e)
\r
1065 ap.alignFrame.cut_actionPerformed(null);
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1068 public void upperCase_actionPerformed(ActionEvent e)
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1070 SequenceGroup sg = ap.av.getSelectionGroup();
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1074 for(int g=0; g<sg.getSize(); g++)
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1076 sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
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1081 public void lowerCase_actionPerformed(ActionEvent e)
\r
1083 SequenceGroup sg = ap.av.getSelectionGroup();
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1087 for(int g=0; g<sg.getSize(); g++)
\r
1089 sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
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1094 public void toggle_actionPerformed(ActionEvent e)
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1096 SequenceGroup sg = ap.av.getSelectionGroup();
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1100 for (int g = 0; g < sg.getSize(); g++)
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1102 sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
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