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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27 import jalview.io.*;
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29 import jalview.schemes.*;
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32 import java.awt.event.*;
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34 import javax.swing.*;
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41 * @version $Revision$
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43 public class PopupMenu extends JPopupMenu
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45 JMenu groupMenu = new JMenu();
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46 JMenuItem groupName = new JMenuItem();
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47 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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48 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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49 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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55 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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56 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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59 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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60 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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62 JMenu sequenceMenu = new JMenu();
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63 JMenuItem sequenceName = new JMenuItem();
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65 JMenuItem unGroupMenuItem = new JMenuItem();
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66 JMenuItem outline = new JMenuItem();
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67 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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68 JMenu colourMenu = new JMenu();
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69 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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70 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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71 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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74 * Creates a new PopupMenu object.
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76 * @param ap DOCUMENT ME!
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77 * @param seq DOCUMENT ME!
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79 public PopupMenu(final AlignmentPanel ap, Sequence seq)
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81 ///////////////////////////////////////////////////////////
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82 // If this is activated from the sequence panel, the user may want to
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83 // edit or annotate a particular residue. Therefore display the residue menu
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85 // If from the IDPanel, we must display the sequence menu
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86 //////////////////////////////////////////////////////////
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90 ButtonGroup colours = new ButtonGroup();
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91 colours.add(noColourmenuItem);
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92 colours.add(clustalColour);
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93 colours.add(zappoColour);
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94 colours.add(taylorColour);
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95 colours.add(hydrophobicityColour);
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96 colours.add(helixColour);
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97 colours.add(strandColour);
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98 colours.add(turnColour);
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99 colours.add(buriedColour);
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100 colours.add(abovePIDColour);
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101 colours.add(userDefinedColour);
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102 colours.add(PIDColour);
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103 colours.add(BLOSUM62Colour);
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109 catch (Exception e)
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111 e.printStackTrace();
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116 && seq.getDatasetSequence().getPDBId() != null)
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118 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements();
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119 while(e.hasMoreElements())
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122 final PDBEntry pdb = (PDBEntry)e.nextElement();
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123 JMenuItem pdbMenuItem = new JMenuItem();
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124 pdbMenuItem.setText("View PDB entry: "+pdb.getId());
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125 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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127 public void actionPerformed(ActionEvent e)
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129 PDBViewer viewer = new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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132 sequenceMenu.add(pdbMenuItem);
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137 SequenceGroup sg = ap.av.getSelectionGroup();
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141 groupName.setText(sg.getName());
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143 if (sg.cs instanceof ZappoColourScheme)
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145 zappoColour.setSelected(true);
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147 else if (sg.cs instanceof TaylorColourScheme)
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149 taylorColour.setSelected(true);
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151 else if (sg.cs instanceof PIDColourScheme)
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153 PIDColour.setSelected(true);
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155 else if (sg.cs instanceof Blosum62ColourScheme)
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157 BLOSUM62Colour.setSelected(true);
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159 else if (sg.cs instanceof UserColourScheme)
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161 userDefinedColour.setSelected(true);
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163 else if (sg.cs instanceof HydrophobicColourScheme)
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165 hydrophobicityColour.setSelected(true);
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167 else if (sg.cs instanceof HelixColourScheme)
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169 helixColour.setSelected(true);
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171 else if (sg.cs instanceof StrandColourScheme)
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173 strandColour.setSelected(true);
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175 else if (sg.cs instanceof TurnColourScheme)
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177 turnColour.setSelected(true);
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179 else if (sg.cs instanceof BuriedColourScheme)
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181 buriedColour.setSelected(true);
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183 else if (sg.cs instanceof ClustalxColourScheme)
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185 clustalColour.setSelected(true);
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189 noColourmenuItem.setSelected(true);
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192 if (sg.cs!=null && sg.cs.conservationApplied())
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194 conservationMenuItem.setSelected(true);
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197 showText.setSelected(sg.getDisplayText());
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198 showColourText.setSelected(sg.getColourText());
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199 showBoxes.setSelected(sg.getDisplayBoxes());
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202 if (!ap.av.alignment.getGroups().contains(sg))
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204 unGroupMenuItem.setVisible(false);
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208 groupMenu.insertSeparator(3);
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213 sequenceMenu.setVisible(false);
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217 java.util.Vector links = Preferences.sequenceURLLinks;
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219 JMenu linkMenu = new JMenu("Link");
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221 for(int i=0; i<links.size(); i++)
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223 String link = links.elementAt(i).toString();
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225 item = new JMenuItem(link.substring(0, link.indexOf("|")));
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227 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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228 + sequence.getName() +
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229 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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232 item.addActionListener(new java.awt.event.ActionListener()
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234 public void actionPerformed(ActionEvent e)
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240 linkMenu.add(item);
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249 * @throws Exception DOCUMENT ME!
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251 private void jbInit() throws Exception
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253 groupMenu.setText("Group");
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254 groupMenu.setText("Define");
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255 groupName.setText("Name");
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256 groupName.addActionListener(new java.awt.event.ActionListener()
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258 public void actionPerformed(ActionEvent e)
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260 groupName_actionPerformed(e);
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263 sequenceMenu.setText("Sequence");
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264 sequenceName.setText("Edit name");
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265 sequenceName.addActionListener(new java.awt.event.ActionListener()
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267 public void actionPerformed(ActionEvent e)
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269 sequenceName_actionPerformed(e);
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272 PIDColour.setFocusPainted(false);
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273 unGroupMenuItem.setText("Remove Group");
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274 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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276 public void actionPerformed(ActionEvent e)
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278 unGroupMenuItem_actionPerformed(e);
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282 outline.setText("Border colour");
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283 outline.addActionListener(new java.awt.event.ActionListener()
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285 public void actionPerformed(ActionEvent e)
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287 outline_actionPerformed(e);
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290 nucleotideMenuItem.setText("Nucleotide");
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291 nucleotideMenuItem.addActionListener(new ActionListener()
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293 public void actionPerformed(ActionEvent e)
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295 nucleotideMenuItem_actionPerformed(e);
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298 colourMenu.setText("Group Colour");
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299 showBoxes.setText("Boxes");
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300 showBoxes.setState(true);
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301 showBoxes.addActionListener(new ActionListener()
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303 public void actionPerformed(ActionEvent e)
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305 showBoxes_actionPerformed(e);
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308 showText.setText("Text");
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309 showText.setState(true);
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310 showText.addActionListener(new ActionListener()
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312 public void actionPerformed(ActionEvent e)
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314 showText_actionPerformed(e);
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317 showColourText.setText("Colour Text");
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318 showColourText.addActionListener(new ActionListener()
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320 public void actionPerformed(ActionEvent e)
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322 showColourText_actionPerformed(e);
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327 groupMenu.add(groupName);
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328 groupMenu.addSeparator();
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329 groupMenu.add(unGroupMenuItem);
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330 groupMenu.add(colourMenu);
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331 groupMenu.addSeparator();
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332 groupMenu.add(showBoxes);
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333 groupMenu.add(showText);
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334 groupMenu.add(showColourText);
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335 groupMenu.addSeparator();
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336 groupMenu.add(outline);
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337 sequenceMenu.add(sequenceName);
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338 colourMenu.add(noColourmenuItem);
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339 colourMenu.add(clustalColour);
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340 colourMenu.add(BLOSUM62Colour);
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341 colourMenu.add(PIDColour);
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342 colourMenu.add(zappoColour);
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343 colourMenu.add(taylorColour);
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344 colourMenu.add(hydrophobicityColour);
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345 colourMenu.add(helixColour);
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346 colourMenu.add(strandColour);
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347 colourMenu.add(turnColour);
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348 colourMenu.add(buriedColour);
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349 colourMenu.add(nucleotideMenuItem);
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350 colourMenu.add(userDefinedColour);
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352 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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354 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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355 getUserColourSchemes().keys();
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357 while (userColours.hasMoreElements())
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359 JMenuItem item = new JMenuItem(userColours.
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360 nextElement().toString());
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361 item.addActionListener(new ActionListener()
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363 public void actionPerformed(ActionEvent evt)
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365 userDefinedColour_actionPerformed(evt);
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368 colourMenu.add(item);
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373 colourMenu.addSeparator();
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374 colourMenu.add(abovePIDColour);
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375 colourMenu.add(conservationMenuItem);
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376 noColourmenuItem.setText("None");
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377 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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379 public void actionPerformed(ActionEvent e)
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381 noColourmenuItem_actionPerformed(e);
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385 clustalColour.setText("Clustalx colours");
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386 clustalColour.addActionListener(new java.awt.event.ActionListener()
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388 public void actionPerformed(ActionEvent e)
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390 clustalColour_actionPerformed(e);
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393 zappoColour.setText("Zappo");
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394 zappoColour.addActionListener(new java.awt.event.ActionListener()
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396 public void actionPerformed(ActionEvent e)
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398 zappoColour_actionPerformed(e);
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401 taylorColour.setText("Taylor");
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402 taylorColour.addActionListener(new java.awt.event.ActionListener()
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404 public void actionPerformed(ActionEvent e)
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406 taylorColour_actionPerformed(e);
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409 hydrophobicityColour.setText("Hydrophobicity");
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410 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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412 public void actionPerformed(ActionEvent e)
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414 hydrophobicityColour_actionPerformed(e);
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417 helixColour.setText("Helix propensity");
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418 helixColour.addActionListener(new java.awt.event.ActionListener()
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420 public void actionPerformed(ActionEvent e)
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422 helixColour_actionPerformed(e);
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425 strandColour.setText("Strand propensity");
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426 strandColour.addActionListener(new java.awt.event.ActionListener()
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428 public void actionPerformed(ActionEvent e)
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430 strandColour_actionPerformed(e);
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433 turnColour.setText("Turn propensity");
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434 turnColour.addActionListener(new java.awt.event.ActionListener()
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436 public void actionPerformed(ActionEvent e)
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438 turnColour_actionPerformed(e);
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441 buriedColour.setText("Buried Index");
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442 buriedColour.addActionListener(new java.awt.event.ActionListener()
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444 public void actionPerformed(ActionEvent e)
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446 buriedColour_actionPerformed(e);
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449 abovePIDColour.setText("Above % Identity");
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450 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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452 public void actionPerformed(ActionEvent e)
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454 abovePIDColour_actionPerformed(e);
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457 userDefinedColour.setText("User Defined...");
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458 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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460 public void actionPerformed(ActionEvent e)
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462 userDefinedColour_actionPerformed(e);
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465 PIDColour.setText("Percentage Identity");
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466 PIDColour.addActionListener(new java.awt.event.ActionListener()
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468 public void actionPerformed(ActionEvent e)
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470 PIDColour_actionPerformed(e);
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473 BLOSUM62Colour.setText("BLOSUM62");
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474 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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476 public void actionPerformed(ActionEvent e)
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478 BLOSUM62Colour_actionPerformed(e);
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481 conservationMenuItem.setText("Conservation");
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482 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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484 public void actionPerformed(ActionEvent e)
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486 conservationMenuItem_actionPerformed(e);
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496 SequenceGroup sg = getGroup();
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499 SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
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501 if (superG != null)
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503 superG.setSuperGroupProperties(sg);
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506 if (ap.overviewPanel != null)
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507 ap.overviewPanel.updateOverviewImage();
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509 ap.seqPanel.repaint();
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515 * @param e DOCUMENT ME!
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517 protected void clustalColour_actionPerformed(ActionEvent e)
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519 SequenceGroup sg = getGroup();
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520 sg.cs = new ClustalxColourScheme(sg.sequences,
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521 ap.av.alignment.getWidth());
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528 * @param e DOCUMENT ME!
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530 protected void zappoColour_actionPerformed(ActionEvent e)
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532 getGroup().cs = new ZappoColourScheme();
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539 * @param e DOCUMENT ME!
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541 protected void taylorColour_actionPerformed(ActionEvent e)
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543 getGroup().cs = new TaylorColourScheme();
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550 * @param e DOCUMENT ME!
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552 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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554 getGroup().cs = new HydrophobicColourScheme();
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561 * @param e DOCUMENT ME!
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563 protected void helixColour_actionPerformed(ActionEvent e)
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565 getGroup().cs = new HelixColourScheme();
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572 * @param e DOCUMENT ME!
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574 protected void strandColour_actionPerformed(ActionEvent e)
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576 getGroup().cs = new StrandColourScheme();
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583 * @param e DOCUMENT ME!
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585 protected void turnColour_actionPerformed(ActionEvent e)
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587 getGroup().cs = new TurnColourScheme();
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594 * @param e DOCUMENT ME!
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596 protected void buriedColour_actionPerformed(ActionEvent e)
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598 getGroup().cs = new BuriedColourScheme();
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605 * @param e DOCUMENT ME!
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607 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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609 getGroup().cs = new NucleotideColourScheme();
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616 * @param e DOCUMENT ME!
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618 protected void abovePIDColour_actionPerformed(ActionEvent e)
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620 SequenceGroup sg = getGroup();
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624 if (abovePIDColour.isSelected())
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626 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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627 ap.av.alignment.getWidth()));
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629 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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630 getGroup().getName());
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632 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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634 SliderPanel.showPIDSlider();
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636 else // remove PIDColouring
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638 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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647 * @param e DOCUMENT ME!
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649 protected void userDefinedColour_actionPerformed(ActionEvent e)
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651 SequenceGroup sg = getGroup();
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653 if (e.getActionCommand().equals("User Defined..."))
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654 new UserDefinedColours(ap, sg);
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657 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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658 getUserColourSchemes().get(e.getActionCommand());
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666 * @param e DOCUMENT ME!
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668 protected void PIDColour_actionPerformed(ActionEvent e)
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670 SequenceGroup sg = getGroup();
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671 sg.cs = new PIDColourScheme();
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672 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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673 ap.av.alignment.getWidth()));
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680 * @param e DOCUMENT ME!
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682 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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684 SequenceGroup sg = getGroup();
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686 sg.cs = new Blosum62ColourScheme();
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688 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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689 ap.av.alignment.getWidth()));
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697 * @param e DOCUMENT ME!
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699 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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701 getGroup().cs = null;
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708 * @param e DOCUMENT ME!
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710 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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712 SequenceGroup sg = getGroup();
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716 if (conservationMenuItem.isSelected())
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718 Conservation c = new Conservation("Group",
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719 ResidueProperties.propHash, 3, sg.sequences, 0,
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720 ap.av.alignment.getWidth());
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723 c.verdict(false, ap.av.ConsPercGaps);
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725 sg.cs.setConservation(c);
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727 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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728 SliderPanel.showConservationSlider();
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730 else // remove ConservationColouring
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732 sg.cs.setConservation(null);
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741 * @param e DOCUMENT ME!
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743 protected void groupName_actionPerformed(ActionEvent e)
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745 SequenceGroup sg = getGroup();
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746 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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747 "Enter new group name", "Edit group name",
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748 JOptionPane.QUESTION_MESSAGE);
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756 groupName.setText(reply);
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762 * @param e DOCUMENT ME!
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764 protected void analyze_actionPerformed(ActionEvent e)
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766 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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767 JInternalFrame frame = new JInternalFrame();
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768 frame.setContentPane(cap);
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769 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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771 SequenceGroup sg = getGroup();
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772 StringBuffer sb = new StringBuffer();
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774 for (int i = 0; i < sg.sequences.size(); i++)
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776 Sequence tmp = (Sequence) sg.sequences.get(i);
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777 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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781 sb.append("Something amazing will happen soon");
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782 cap.setText(sb.toString());
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788 * @return DOCUMENT ME!
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790 SequenceGroup getGroup()
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792 SequenceGroup sg = ap.av.getSelectionGroup();
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793 // this method won't add a new group if it already exists
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795 ap.av.alignment.addGroup(sg);
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803 * @param e DOCUMENT ME!
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805 void sequenceName_actionPerformed(ActionEvent e)
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807 String id = sequence.getDisplayId(false, false);
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808 String s = (String) JOptionPane.showInternalInputDialog(ap,
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809 "Edit sequence name",
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810 "Edit sequence name (" + sequence.getName() + ")",
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811 JOptionPane.PLAIN_MESSAGE, null, null, id);
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815 if (s.indexOf(" ") > -1)
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817 JOptionPane.showMessageDialog(ap,
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818 "Spaces have been converted to \"_\"",
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819 "No spaces allowed in Sequence Name",
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820 JOptionPane.WARNING_MESSAGE);
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823 s = s.replace(' ', '_');
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824 sequence.setName(s);
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832 * @param e DOCUMENT ME!
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834 void unGroupMenuItem_actionPerformed(ActionEvent e)
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836 SequenceGroup sg = ap.av.getSelectionGroup();
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837 ap.av.alignment.deleteGroup(sg);
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838 ap.av.setSelectionGroup(null);
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846 * @param e DOCUMENT ME!
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848 protected void outline_actionPerformed(ActionEvent e)
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850 SequenceGroup sg = getGroup();
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851 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
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856 sg.setOutlineColour(col);
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865 * @param e DOCUMENT ME!
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867 public void showBoxes_actionPerformed(ActionEvent e)
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869 getGroup().setDisplayBoxes(showBoxes.isSelected());
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876 * @param e DOCUMENT ME!
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878 public void showText_actionPerformed(ActionEvent e)
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880 getGroup().setDisplayText(showText.isSelected());
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887 * @param e DOCUMENT ME!
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889 public void showColourText_actionPerformed(ActionEvent e)
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891 getGroup().setColourText(showColourText.isSelected());
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895 public void showLink(String url)
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899 jalview.util.BrowserLauncher.openURL(url);
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901 catch (Exception ex)
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903 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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904 "Unixers: Couldn't find default web browser."
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905 +"\nAdd the full path to your browser in Preferences.",
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906 "Web browser not found", JOptionPane.WARNING_MESSAGE );
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909 ex.printStackTrace();
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