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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40 * @version $Revision$
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42 public class PopupMenu extends JPopupMenu
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44 JMenu groupMenu = new JMenu();
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45 JMenuItem groupName = new JMenuItem();
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46 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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47 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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48 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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49 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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54 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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55 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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58 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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59 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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61 JMenu sequenceMenu = new JMenu();
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62 JMenuItem sequenceName = new JMenuItem();
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64 JMenuItem unGroupMenuItem = new JMenuItem();
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65 JMenuItem outline = new JMenuItem();
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66 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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67 JMenu colourMenu = new JMenu();
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68 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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69 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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70 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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71 JMenu jMenu1 = new JMenu();
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72 JMenuItem cut = new JMenuItem();
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73 JMenuItem copy = new JMenuItem();
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74 JMenuItem upperCase = new JMenuItem();
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75 JMenuItem lowerCase = new JMenuItem();
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78 * Creates a new PopupMenu object.
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80 * @param ap DOCUMENT ME!
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81 * @param seq DOCUMENT ME!
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83 public PopupMenu(final AlignmentPanel ap, Sequence seq)
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85 ///////////////////////////////////////////////////////////
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86 // If this is activated from the sequence panel, the user may want to
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87 // edit or annotate a particular residue. Therefore display the residue menu
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89 // If from the IDPanel, we must display the sequence menu
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90 //////////////////////////////////////////////////////////
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94 ButtonGroup colours = new ButtonGroup();
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95 colours.add(noColourmenuItem);
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96 colours.add(clustalColour);
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97 colours.add(zappoColour);
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98 colours.add(taylorColour);
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99 colours.add(hydrophobicityColour);
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100 colours.add(helixColour);
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101 colours.add(strandColour);
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102 colours.add(turnColour);
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103 colours.add(buriedColour);
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104 colours.add(abovePIDColour);
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105 colours.add(userDefinedColour);
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106 colours.add(PIDColour);
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107 colours.add(BLOSUM62Colour);
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113 catch (Exception e)
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115 e.printStackTrace();
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121 JMenuItem menuItem;
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122 if( seq.getDatasetSequence().getPDBId() != null)
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124 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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126 while (e.hasMoreElements())
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128 final PDBEntry pdb = (PDBEntry) e.nextElement();
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130 menuItem = new JMenuItem();
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131 menuItem.setText("View PDB entry: " + pdb.getId());
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132 menuItem.addActionListener(new java.awt.event.ActionListener()
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134 public void actionPerformed(ActionEvent e)
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136 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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139 sequenceMenu.add(menuItem);
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143 /* menuItem = new JMenuItem("Hide Sequences");
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144 menuItem.addActionListener(new java.awt.event.ActionListener()
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146 public void actionPerformed(ActionEvent e)
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148 hideSequences(false);
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151 sequenceMenu.add(menuItem);
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153 if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)
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155 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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156 menuItem.addActionListener(new java.awt.event.ActionListener()
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158 public void actionPerformed(ActionEvent e)
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160 hideSequences(true);
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163 sequenceMenu.add(menuItem);
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171 SequenceGroup sg = ap.av.getSelectionGroup();
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175 groupName.setText(sg.getName());
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177 if (sg.cs instanceof ZappoColourScheme)
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179 zappoColour.setSelected(true);
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181 else if (sg.cs instanceof TaylorColourScheme)
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183 taylorColour.setSelected(true);
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185 else if (sg.cs instanceof PIDColourScheme)
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187 PIDColour.setSelected(true);
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189 else if (sg.cs instanceof Blosum62ColourScheme)
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191 BLOSUM62Colour.setSelected(true);
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193 else if (sg.cs instanceof UserColourScheme)
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195 userDefinedColour.setSelected(true);
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197 else if (sg.cs instanceof HydrophobicColourScheme)
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199 hydrophobicityColour.setSelected(true);
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201 else if (sg.cs instanceof HelixColourScheme)
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203 helixColour.setSelected(true);
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205 else if (sg.cs instanceof StrandColourScheme)
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207 strandColour.setSelected(true);
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209 else if (sg.cs instanceof TurnColourScheme)
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211 turnColour.setSelected(true);
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213 else if (sg.cs instanceof BuriedColourScheme)
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215 buriedColour.setSelected(true);
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217 else if (sg.cs instanceof ClustalxColourScheme)
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219 clustalColour.setSelected(true);
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223 noColourmenuItem.setSelected(true);
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226 if (sg.cs!=null && sg.cs.conservationApplied())
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228 conservationMenuItem.setSelected(true);
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231 showText.setSelected(sg.getDisplayText());
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232 showColourText.setSelected(sg.getColourText());
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233 showBoxes.setSelected(sg.getDisplayBoxes());
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236 groupMenu.setVisible(false);
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238 if (!ap.av.alignment.getGroups().contains(sg))
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240 unGroupMenuItem.setVisible(false);
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244 groupMenu.insertSeparator(3);
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249 sequenceMenu.setVisible(false);
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253 java.util.Vector links = Preferences.sequenceURLLinks;
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255 JMenu linkMenu = new JMenu("Link");
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257 for(int i=0; i<links.size(); i++)
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259 String link = links.elementAt(i).toString();
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261 item = new JMenuItem(link.substring(0, link.indexOf("|")));
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262 String id = sequence.getName();
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263 if(id.indexOf("|")>-1)
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264 id = id.substring(id.lastIndexOf("|")+1);
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266 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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268 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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271 item.addActionListener(new java.awt.event.ActionListener()
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273 public void actionPerformed(ActionEvent e)
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279 linkMenu.add(item);
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289 * @throws Exception DOCUMENT ME!
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291 private void jbInit() throws Exception
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293 groupMenu.setText("Group");
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294 groupMenu.setText("Group");
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295 groupName.setText("Name");
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296 groupName.addActionListener(new java.awt.event.ActionListener()
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298 public void actionPerformed(ActionEvent e)
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300 groupName_actionPerformed(e);
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303 sequenceMenu.setText("Sequence");
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304 sequenceName.setText("Edit Name/Description");
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305 sequenceName.addActionListener(new java.awt.event.ActionListener()
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307 public void actionPerformed(ActionEvent e)
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309 sequenceName_actionPerformed(e);
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312 PIDColour.setFocusPainted(false);
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313 unGroupMenuItem.setText("Remove Group");
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314 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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316 public void actionPerformed(ActionEvent e)
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318 unGroupMenuItem_actionPerformed(e);
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322 outline.setText("Border colour");
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323 outline.addActionListener(new java.awt.event.ActionListener()
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325 public void actionPerformed(ActionEvent e)
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327 outline_actionPerformed(e);
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330 nucleotideMenuItem.setText("Nucleotide");
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331 nucleotideMenuItem.addActionListener(new ActionListener()
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333 public void actionPerformed(ActionEvent e)
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335 nucleotideMenuItem_actionPerformed(e);
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338 colourMenu.setText("Group Colour");
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339 showBoxes.setText("Boxes");
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340 showBoxes.setState(true);
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341 showBoxes.addActionListener(new ActionListener()
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343 public void actionPerformed(ActionEvent e)
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345 showBoxes_actionPerformed(e);
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348 showText.setText("Text");
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349 showText.setState(true);
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350 showText.addActionListener(new ActionListener()
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352 public void actionPerformed(ActionEvent e)
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354 showText_actionPerformed(e);
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357 showColourText.setText("Colour Text");
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358 showColourText.addActionListener(new ActionListener()
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360 public void actionPerformed(ActionEvent e)
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362 showColourText_actionPerformed(e);
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365 jMenu1.setText("Edit");
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366 cut.setText("Cut");
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367 cut.addActionListener(new ActionListener()
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369 public void actionPerformed(ActionEvent e)
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371 cut_actionPerformed(e);
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374 upperCase.setText("To Upper Case");
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375 upperCase.addActionListener(new ActionListener()
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377 public void actionPerformed(ActionEvent e)
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379 upperCase_actionPerformed(e);
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382 copy.setText("Copy");
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383 copy.addActionListener(new ActionListener()
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385 public void actionPerformed(ActionEvent e)
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387 copy_actionPerformed(e);
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390 lowerCase.setText("To Lower Case");
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391 lowerCase.addActionListener(new ActionListener()
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393 public void actionPerformed(ActionEvent e)
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395 lowerCase_actionPerformed(e);
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401 groupMenu.add(groupName);
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402 groupMenu.addSeparator();
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403 groupMenu.add(unGroupMenuItem);
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404 groupMenu.add(colourMenu);
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405 groupMenu.addSeparator();
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406 groupMenu.add(showBoxes);
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407 groupMenu.add(showText);
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408 groupMenu.add(showColourText);
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409 groupMenu.addSeparator();
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410 groupMenu.add(outline);
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411 sequenceMenu.add(sequenceName);
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412 colourMenu.add(noColourmenuItem);
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413 colourMenu.add(clustalColour);
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414 colourMenu.add(BLOSUM62Colour);
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415 colourMenu.add(PIDColour);
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416 colourMenu.add(zappoColour);
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417 colourMenu.add(taylorColour);
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418 colourMenu.add(hydrophobicityColour);
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419 colourMenu.add(helixColour);
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420 colourMenu.add(strandColour);
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421 colourMenu.add(turnColour);
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422 colourMenu.add(buriedColour);
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423 colourMenu.add(nucleotideMenuItem);
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424 colourMenu.add(userDefinedColour);
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426 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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428 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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429 getUserColourSchemes().keys();
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431 while (userColours.hasMoreElements())
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433 JMenuItem item = new JMenuItem(userColours.
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434 nextElement().toString());
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435 item.addActionListener(new ActionListener()
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437 public void actionPerformed(ActionEvent evt)
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439 userDefinedColour_actionPerformed(evt);
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442 colourMenu.add(item);
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447 colourMenu.addSeparator();
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448 colourMenu.add(abovePIDColour);
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449 colourMenu.add(conservationMenuItem);
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452 jMenu1.add(upperCase);
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453 jMenu1.add(lowerCase);
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454 noColourmenuItem.setText("None");
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455 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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457 public void actionPerformed(ActionEvent e)
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459 noColourmenuItem_actionPerformed(e);
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463 clustalColour.setText("Clustalx colours");
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464 clustalColour.addActionListener(new java.awt.event.ActionListener()
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466 public void actionPerformed(ActionEvent e)
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468 clustalColour_actionPerformed(e);
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471 zappoColour.setText("Zappo");
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472 zappoColour.addActionListener(new java.awt.event.ActionListener()
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474 public void actionPerformed(ActionEvent e)
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476 zappoColour_actionPerformed(e);
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479 taylorColour.setText("Taylor");
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480 taylorColour.addActionListener(new java.awt.event.ActionListener()
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482 public void actionPerformed(ActionEvent e)
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484 taylorColour_actionPerformed(e);
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487 hydrophobicityColour.setText("Hydrophobicity");
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488 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 hydrophobicityColour_actionPerformed(e);
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495 helixColour.setText("Helix propensity");
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496 helixColour.addActionListener(new java.awt.event.ActionListener()
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498 public void actionPerformed(ActionEvent e)
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500 helixColour_actionPerformed(e);
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503 strandColour.setText("Strand propensity");
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504 strandColour.addActionListener(new java.awt.event.ActionListener()
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506 public void actionPerformed(ActionEvent e)
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508 strandColour_actionPerformed(e);
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511 turnColour.setText("Turn propensity");
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512 turnColour.addActionListener(new java.awt.event.ActionListener()
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514 public void actionPerformed(ActionEvent e)
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516 turnColour_actionPerformed(e);
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519 buriedColour.setText("Buried Index");
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520 buriedColour.addActionListener(new java.awt.event.ActionListener()
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522 public void actionPerformed(ActionEvent e)
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524 buriedColour_actionPerformed(e);
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527 abovePIDColour.setText("Above % Identity");
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528 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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530 public void actionPerformed(ActionEvent e)
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532 abovePIDColour_actionPerformed(e);
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535 userDefinedColour.setText("User Defined...");
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536 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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538 public void actionPerformed(ActionEvent e)
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540 userDefinedColour_actionPerformed(e);
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543 PIDColour.setText("Percentage Identity");
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544 PIDColour.addActionListener(new java.awt.event.ActionListener()
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546 public void actionPerformed(ActionEvent e)
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548 PIDColour_actionPerformed(e);
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551 BLOSUM62Colour.setText("BLOSUM62");
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552 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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554 public void actionPerformed(ActionEvent e)
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556 BLOSUM62Colour_actionPerformed(e);
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559 conservationMenuItem.setText("Conservation");
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560 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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562 public void actionPerformed(ActionEvent e)
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564 conservationMenuItem_actionPerformed(e);
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574 if (ap.overviewPanel != null)
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575 ap.overviewPanel.updateOverviewImage();
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577 ap.seqPanel.repaint();
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583 * @param e DOCUMENT ME!
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585 protected void clustalColour_actionPerformed(ActionEvent e)
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587 SequenceGroup sg = getGroup();
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588 sg.cs = new ClustalxColourScheme(sg.sequences,
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589 ap.av.alignment.getWidth());
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596 * @param e DOCUMENT ME!
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598 protected void zappoColour_actionPerformed(ActionEvent e)
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600 getGroup().cs = new ZappoColourScheme();
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607 * @param e DOCUMENT ME!
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609 protected void taylorColour_actionPerformed(ActionEvent e)
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611 getGroup().cs = new TaylorColourScheme();
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618 * @param e DOCUMENT ME!
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620 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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622 getGroup().cs = new HydrophobicColourScheme();
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629 * @param e DOCUMENT ME!
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631 protected void helixColour_actionPerformed(ActionEvent e)
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633 getGroup().cs = new HelixColourScheme();
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640 * @param e DOCUMENT ME!
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642 protected void strandColour_actionPerformed(ActionEvent e)
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644 getGroup().cs = new StrandColourScheme();
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651 * @param e DOCUMENT ME!
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653 protected void turnColour_actionPerformed(ActionEvent e)
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655 getGroup().cs = new TurnColourScheme();
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662 * @param e DOCUMENT ME!
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664 protected void buriedColour_actionPerformed(ActionEvent e)
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666 getGroup().cs = new BuriedColourScheme();
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673 * @param e DOCUMENT ME!
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675 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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677 getGroup().cs = new NucleotideColourScheme();
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684 * @param e DOCUMENT ME!
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686 protected void abovePIDColour_actionPerformed(ActionEvent e)
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688 SequenceGroup sg = getGroup();
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692 if (abovePIDColour.isSelected())
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694 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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695 ap.av.alignment.getWidth()));
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697 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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698 getGroup().getName());
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700 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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702 SliderPanel.showPIDSlider();
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704 else // remove PIDColouring
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706 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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715 * @param e DOCUMENT ME!
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717 protected void userDefinedColour_actionPerformed(ActionEvent e)
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719 SequenceGroup sg = getGroup();
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721 if (e.getActionCommand().equals("User Defined..."))
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722 new UserDefinedColours(ap, sg);
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725 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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726 getUserColourSchemes().get(e.getActionCommand());
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734 * @param e DOCUMENT ME!
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736 protected void PIDColour_actionPerformed(ActionEvent e)
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738 SequenceGroup sg = getGroup();
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739 sg.cs = new PIDColourScheme();
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740 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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741 ap.av.alignment.getWidth()));
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748 * @param e DOCUMENT ME!
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750 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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752 SequenceGroup sg = getGroup();
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754 sg.cs = new Blosum62ColourScheme();
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756 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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757 ap.av.alignment.getWidth()));
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765 * @param e DOCUMENT ME!
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767 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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769 getGroup().cs = null;
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776 * @param e DOCUMENT ME!
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778 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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780 SequenceGroup sg = getGroup();
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784 if (conservationMenuItem.isSelected())
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786 Conservation c = new Conservation("Group",
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787 ResidueProperties.propHash, 3, sg.sequences, 0,
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788 ap.av.alignment.getWidth());
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791 c.verdict(false, ap.av.ConsPercGaps);
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793 sg.cs.setConservation(c);
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795 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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796 SliderPanel.showConservationSlider();
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798 else // remove ConservationColouring
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800 sg.cs.setConservation(null);
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809 * @param e DOCUMENT ME!
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811 protected void groupName_actionPerformed(ActionEvent e)
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813 SequenceGroup sg = getGroup();
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814 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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815 "Enter new group name", "Edit group name",
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816 JOptionPane.QUESTION_MESSAGE);
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824 groupName.setText(reply);
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830 * @param e DOCUMENT ME!
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832 protected void analyze_actionPerformed(ActionEvent e)
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834 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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835 JInternalFrame frame = new JInternalFrame();
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836 frame.setContentPane(cap);
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837 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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839 SequenceGroup sg = getGroup();
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840 StringBuffer sb = new StringBuffer();
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842 for (int i = 0; i < sg.sequences.size(); i++)
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844 Sequence tmp = (Sequence) sg.sequences.get(i);
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845 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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849 sb.append("Something amazing will happen soon");
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850 cap.setText(sb.toString());
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856 * @return DOCUMENT ME!
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858 SequenceGroup getGroup()
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860 SequenceGroup sg = ap.av.getSelectionGroup();
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861 // this method won't add a new group if it already exists
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863 ap.av.alignment.addGroup(sg);
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871 * @param e DOCUMENT ME!
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873 void sequenceName_actionPerformed(ActionEvent e)
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875 JLabel idlabel = new JLabel( " Sequence Name ");
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876 JLabel desclabel = new JLabel("Sequence Description ");
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877 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
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878 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
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879 JTextField id = new JTextField(sequence.getName(), 40);
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880 JTextField description = new JTextField(sequence.getDescription(), 40);
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881 JPanel panel = new JPanel(new BorderLayout());
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882 JPanel panel2 = new JPanel(new BorderLayout());
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883 panel2.add(idlabel, BorderLayout.WEST);
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884 panel2.add(id, BorderLayout.CENTER);
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885 panel.add(panel2, BorderLayout.NORTH);
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886 panel2 = new JPanel(new BorderLayout());
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887 panel2.add(desclabel, BorderLayout.WEST);
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888 panel2.add(description, BorderLayout.CENTER);
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889 panel.add(panel2, BorderLayout.SOUTH);
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892 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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893 panel, "Edit Sequence Name/Description",
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894 JOptionPane.OK_CANCEL_OPTION );
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897 if (reply != JOptionPane.OK_OPTION )
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902 String s = id.getText();
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906 if (s.indexOf(" ") > -1)
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908 JOptionPane.showMessageDialog(ap,
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909 "Spaces have been converted to \"_\"",
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910 "No spaces allowed in Sequence Name",
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911 JOptionPane.WARNING_MESSAGE);
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914 s = s.replace(' ', '_');
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915 sequence.getDatasetSequence().setName(s);
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916 sequence.setName(s);
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920 sequence.getDatasetSequence().setDescription(description.getText());
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921 sequence.setDescription(description.getText());
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927 * @param e DOCUMENT ME!
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929 void unGroupMenuItem_actionPerformed(ActionEvent e)
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931 SequenceGroup sg = ap.av.getSelectionGroup();
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932 ap.av.alignment.deleteGroup(sg);
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933 ap.av.setSelectionGroup(null);
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941 * @param e DOCUMENT ME!
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943 protected void outline_actionPerformed(ActionEvent e)
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945 SequenceGroup sg = getGroup();
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946 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
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951 sg.setOutlineColour(col);
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960 * @param e DOCUMENT ME!
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962 public void showBoxes_actionPerformed(ActionEvent e)
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964 getGroup().setDisplayBoxes(showBoxes.isSelected());
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971 * @param e DOCUMENT ME!
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973 public void showText_actionPerformed(ActionEvent e)
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975 getGroup().setDisplayText(showText.isSelected());
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982 * @param e DOCUMENT ME!
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984 public void showColourText_actionPerformed(ActionEvent e)
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986 getGroup().setColourText(showColourText.isSelected());
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990 public void showLink(String url)
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994 jalview.util.BrowserLauncher.openURL(url);
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996 catch (Exception ex)
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998 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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999 "Unixers: Couldn't find default web browser."
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1000 +"\nAdd the full path to your browser in Preferences.",
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1001 "Web browser not found", JOptionPane.WARNING_MESSAGE );
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1004 ex.printStackTrace();
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1008 void hideSequences(boolean representGroup)
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1010 SequenceGroup sg = ap.av.getSelectionGroup();
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1011 if(sg==null || sg.getSize()<1)
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1013 ap.av.hideSequence(sequence);
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1018 while(index < sg.sequences.size())
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1020 if(representGroup && sg.getSequenceAt(index)!=sequence)
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1022 sequence.addHiddenSequence(sg.getSequenceAt(index));
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1023 ap.av.hideSequence(sg.getSequenceAt(index));
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1025 else if(!representGroup)
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1027 ap.av.hideSequence(sg.getSequenceAt(index));
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1032 ap.av.setSelectionGroup(null);
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1036 public void copy_actionPerformed(ActionEvent e)
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1038 ap.alignFrame.copy_actionPerformed(null);
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1041 public void cut_actionPerformed(ActionEvent e)
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1043 ap.alignFrame.cut_actionPerformed(null);
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1046 public void upperCase_actionPerformed(ActionEvent e)
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1048 SequenceGroup sg = ap.av.getSelectionGroup();
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1052 for(int g=0; g<sg.getSize(); g++)
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1054 sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
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1059 public void lowerCase_actionPerformed(ActionEvent e)
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1061 SequenceGroup sg = ap.av.getSelectionGroup();
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1065 for(int g=0; g<sg.getSize(); g++)
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1067 sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
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