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 editMenu = 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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237 groupMenu.setVisible(false);
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238 editMenu.setVisible(false);
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241 if (!ap.av.alignment.getGroups().contains(sg))
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243 unGroupMenuItem.setVisible(false);
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247 groupMenu.insertSeparator(3);
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252 sequenceMenu.setVisible(false);
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256 java.util.Vector links = Preferences.sequenceURLLinks;
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258 JMenu linkMenu = new JMenu("Link");
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260 for(int i=0; i<links.size(); i++)
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262 String link = links.elementAt(i).toString();
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264 item = new JMenuItem(link.substring(0, link.indexOf("|")));
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265 String id = sequence.getName();
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266 if(id.indexOf("|")>-1)
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267 id = id.substring(id.lastIndexOf("|")+1);
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269 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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271 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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274 item.addActionListener(new java.awt.event.ActionListener()
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276 public void actionPerformed(ActionEvent e)
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282 linkMenu.add(item);
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292 * @throws Exception DOCUMENT ME!
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294 private void jbInit() throws Exception
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296 groupMenu.setText("Group");
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297 groupMenu.setText("Group");
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298 groupName.setText("Name");
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299 groupName.addActionListener(new java.awt.event.ActionListener()
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301 public void actionPerformed(ActionEvent e)
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303 groupName_actionPerformed(e);
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306 sequenceMenu.setText("Sequence");
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307 sequenceName.setText("Edit Name/Description");
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308 sequenceName.addActionListener(new java.awt.event.ActionListener()
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310 public void actionPerformed(ActionEvent e)
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312 sequenceName_actionPerformed(e);
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315 PIDColour.setFocusPainted(false);
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316 unGroupMenuItem.setText("Remove Group");
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317 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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319 public void actionPerformed(ActionEvent e)
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321 unGroupMenuItem_actionPerformed(e);
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325 outline.setText("Border colour");
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326 outline.addActionListener(new java.awt.event.ActionListener()
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328 public void actionPerformed(ActionEvent e)
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330 outline_actionPerformed(e);
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333 nucleotideMenuItem.setText("Nucleotide");
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334 nucleotideMenuItem.addActionListener(new ActionListener()
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336 public void actionPerformed(ActionEvent e)
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338 nucleotideMenuItem_actionPerformed(e);
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341 colourMenu.setText("Group Colour");
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342 showBoxes.setText("Boxes");
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343 showBoxes.setState(true);
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344 showBoxes.addActionListener(new ActionListener()
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346 public void actionPerformed(ActionEvent e)
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348 showBoxes_actionPerformed(e);
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351 showText.setText("Text");
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352 showText.setState(true);
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353 showText.addActionListener(new ActionListener()
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355 public void actionPerformed(ActionEvent e)
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357 showText_actionPerformed(e);
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360 showColourText.setText("Colour Text");
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361 showColourText.addActionListener(new ActionListener()
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363 public void actionPerformed(ActionEvent e)
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365 showColourText_actionPerformed(e);
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368 editMenu.setText("Edit");
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369 cut.setText("Cut");
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370 cut.addActionListener(new ActionListener()
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372 public void actionPerformed(ActionEvent e)
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374 cut_actionPerformed(e);
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377 upperCase.setText("To Upper Case");
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378 upperCase.addActionListener(new ActionListener()
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380 public void actionPerformed(ActionEvent e)
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382 upperCase_actionPerformed(e);
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385 copy.setText("Copy");
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386 copy.addActionListener(new ActionListener()
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388 public void actionPerformed(ActionEvent e)
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390 copy_actionPerformed(e);
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393 lowerCase.setText("To Lower Case");
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394 lowerCase.addActionListener(new ActionListener()
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396 public void actionPerformed(ActionEvent e)
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398 lowerCase_actionPerformed(e);
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403 this.add(editMenu);
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404 groupMenu.add(groupName);
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405 groupMenu.addSeparator();
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406 groupMenu.add(unGroupMenuItem);
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407 groupMenu.add(colourMenu);
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408 groupMenu.addSeparator();
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409 groupMenu.add(showBoxes);
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410 groupMenu.add(showText);
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411 groupMenu.add(showColourText);
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412 groupMenu.addSeparator();
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413 groupMenu.add(outline);
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414 sequenceMenu.add(sequenceName);
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415 colourMenu.add(noColourmenuItem);
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416 colourMenu.add(clustalColour);
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417 colourMenu.add(BLOSUM62Colour);
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418 colourMenu.add(PIDColour);
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419 colourMenu.add(zappoColour);
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420 colourMenu.add(taylorColour);
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421 colourMenu.add(hydrophobicityColour);
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422 colourMenu.add(helixColour);
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423 colourMenu.add(strandColour);
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424 colourMenu.add(turnColour);
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425 colourMenu.add(buriedColour);
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426 colourMenu.add(nucleotideMenuItem);
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427 colourMenu.add(userDefinedColour);
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429 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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431 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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432 getUserColourSchemes().keys();
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434 while (userColours.hasMoreElements())
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436 JMenuItem item = new JMenuItem(userColours.
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437 nextElement().toString());
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438 item.addActionListener(new ActionListener()
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440 public void actionPerformed(ActionEvent evt)
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442 userDefinedColour_actionPerformed(evt);
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445 colourMenu.add(item);
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450 colourMenu.addSeparator();
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451 colourMenu.add(abovePIDColour);
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452 colourMenu.add(conservationMenuItem);
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453 editMenu.add(copy);
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455 editMenu.add(upperCase);
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456 editMenu.add(lowerCase);
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457 noColourmenuItem.setText("None");
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458 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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460 public void actionPerformed(ActionEvent e)
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462 noColourmenuItem_actionPerformed(e);
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466 clustalColour.setText("Clustalx colours");
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467 clustalColour.addActionListener(new java.awt.event.ActionListener()
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469 public void actionPerformed(ActionEvent e)
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471 clustalColour_actionPerformed(e);
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474 zappoColour.setText("Zappo");
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475 zappoColour.addActionListener(new java.awt.event.ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 zappoColour_actionPerformed(e);
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482 taylorColour.setText("Taylor");
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483 taylorColour.addActionListener(new java.awt.event.ActionListener()
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485 public void actionPerformed(ActionEvent e)
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487 taylorColour_actionPerformed(e);
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490 hydrophobicityColour.setText("Hydrophobicity");
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491 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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493 public void actionPerformed(ActionEvent e)
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495 hydrophobicityColour_actionPerformed(e);
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498 helixColour.setText("Helix propensity");
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499 helixColour.addActionListener(new java.awt.event.ActionListener()
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501 public void actionPerformed(ActionEvent e)
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503 helixColour_actionPerformed(e);
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506 strandColour.setText("Strand propensity");
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507 strandColour.addActionListener(new java.awt.event.ActionListener()
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509 public void actionPerformed(ActionEvent e)
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511 strandColour_actionPerformed(e);
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514 turnColour.setText("Turn propensity");
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515 turnColour.addActionListener(new java.awt.event.ActionListener()
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517 public void actionPerformed(ActionEvent e)
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519 turnColour_actionPerformed(e);
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522 buriedColour.setText("Buried Index");
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523 buriedColour.addActionListener(new java.awt.event.ActionListener()
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525 public void actionPerformed(ActionEvent e)
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527 buriedColour_actionPerformed(e);
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530 abovePIDColour.setText("Above % Identity");
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531 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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533 public void actionPerformed(ActionEvent e)
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535 abovePIDColour_actionPerformed(e);
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538 userDefinedColour.setText("User Defined...");
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539 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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541 public void actionPerformed(ActionEvent e)
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543 userDefinedColour_actionPerformed(e);
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546 PIDColour.setText("Percentage Identity");
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547 PIDColour.addActionListener(new java.awt.event.ActionListener()
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549 public void actionPerformed(ActionEvent e)
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551 PIDColour_actionPerformed(e);
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554 BLOSUM62Colour.setText("BLOSUM62");
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555 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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557 public void actionPerformed(ActionEvent e)
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559 BLOSUM62Colour_actionPerformed(e);
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562 conservationMenuItem.setText("Conservation");
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563 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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565 public void actionPerformed(ActionEvent e)
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567 conservationMenuItem_actionPerformed(e);
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577 if (ap.overviewPanel != null)
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578 ap.overviewPanel.updateOverviewImage();
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580 ap.seqPanel.repaint();
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586 * @param e DOCUMENT ME!
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588 protected void clustalColour_actionPerformed(ActionEvent e)
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590 SequenceGroup sg = getGroup();
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591 sg.cs = new ClustalxColourScheme(sg.sequences,
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592 ap.av.alignment.getWidth());
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599 * @param e DOCUMENT ME!
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601 protected void zappoColour_actionPerformed(ActionEvent e)
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603 getGroup().cs = new ZappoColourScheme();
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610 * @param e DOCUMENT ME!
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612 protected void taylorColour_actionPerformed(ActionEvent e)
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614 getGroup().cs = new TaylorColourScheme();
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621 * @param e DOCUMENT ME!
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623 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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625 getGroup().cs = new HydrophobicColourScheme();
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632 * @param e DOCUMENT ME!
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634 protected void helixColour_actionPerformed(ActionEvent e)
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636 getGroup().cs = new HelixColourScheme();
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643 * @param e DOCUMENT ME!
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645 protected void strandColour_actionPerformed(ActionEvent e)
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647 getGroup().cs = new StrandColourScheme();
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654 * @param e DOCUMENT ME!
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656 protected void turnColour_actionPerformed(ActionEvent e)
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658 getGroup().cs = new TurnColourScheme();
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665 * @param e DOCUMENT ME!
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667 protected void buriedColour_actionPerformed(ActionEvent e)
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669 getGroup().cs = new BuriedColourScheme();
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676 * @param e DOCUMENT ME!
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678 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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680 getGroup().cs = new NucleotideColourScheme();
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687 * @param e DOCUMENT ME!
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689 protected void abovePIDColour_actionPerformed(ActionEvent e)
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691 SequenceGroup sg = getGroup();
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695 if (abovePIDColour.isSelected())
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697 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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698 ap.av.alignment.getWidth()));
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700 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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701 getGroup().getName());
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703 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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705 SliderPanel.showPIDSlider();
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707 else // remove PIDColouring
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709 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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718 * @param e DOCUMENT ME!
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720 protected void userDefinedColour_actionPerformed(ActionEvent e)
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722 SequenceGroup sg = getGroup();
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724 if (e.getActionCommand().equals("User Defined..."))
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725 new UserDefinedColours(ap, sg);
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728 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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729 getUserColourSchemes().get(e.getActionCommand());
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737 * @param e DOCUMENT ME!
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739 protected void PIDColour_actionPerformed(ActionEvent e)
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741 SequenceGroup sg = getGroup();
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742 sg.cs = new PIDColourScheme();
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743 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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744 ap.av.alignment.getWidth()));
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751 * @param e DOCUMENT ME!
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753 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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755 SequenceGroup sg = getGroup();
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757 sg.cs = new Blosum62ColourScheme();
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759 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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760 ap.av.alignment.getWidth()));
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768 * @param e DOCUMENT ME!
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770 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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772 getGroup().cs = null;
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779 * @param e DOCUMENT ME!
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781 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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783 SequenceGroup sg = getGroup();
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787 if (conservationMenuItem.isSelected())
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789 Conservation c = new Conservation("Group",
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790 ResidueProperties.propHash, 3, sg.sequences, 0,
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791 ap.av.alignment.getWidth());
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794 c.verdict(false, ap.av.ConsPercGaps);
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796 sg.cs.setConservation(c);
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798 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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799 SliderPanel.showConservationSlider();
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801 else // remove ConservationColouring
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803 sg.cs.setConservation(null);
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812 * @param e DOCUMENT ME!
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814 protected void groupName_actionPerformed(ActionEvent e)
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816 SequenceGroup sg = getGroup();
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817 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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818 "Enter new group name", "Edit group name",
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819 JOptionPane.QUESTION_MESSAGE);
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827 groupName.setText(reply);
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833 * @param e DOCUMENT ME!
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835 protected void analyze_actionPerformed(ActionEvent e)
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837 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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838 JInternalFrame frame = new JInternalFrame();
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839 frame.setContentPane(cap);
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840 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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842 SequenceGroup sg = getGroup();
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843 StringBuffer sb = new StringBuffer();
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845 for (int i = 0; i < sg.sequences.size(); i++)
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847 Sequence tmp = (Sequence) sg.sequences.get(i);
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848 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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852 sb.append("Something amazing will happen soon");
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853 cap.setText(sb.toString());
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859 * @return DOCUMENT ME!
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861 SequenceGroup getGroup()
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863 SequenceGroup sg = ap.av.getSelectionGroup();
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864 // this method won't add a new group if it already exists
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866 ap.av.alignment.addGroup(sg);
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874 * @param e DOCUMENT ME!
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876 void sequenceName_actionPerformed(ActionEvent e)
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878 JLabel idlabel = new JLabel( " Sequence Name ");
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879 JLabel desclabel = new JLabel("Sequence Description ");
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880 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
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881 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
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882 JTextField id = new JTextField(sequence.getName(), 40);
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883 JTextField description = new JTextField(sequence.getDescription(), 40);
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884 JPanel panel = new JPanel(new BorderLayout());
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885 JPanel panel2 = new JPanel(new BorderLayout());
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886 panel2.add(idlabel, BorderLayout.WEST);
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887 panel2.add(id, BorderLayout.CENTER);
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888 panel.add(panel2, BorderLayout.NORTH);
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889 panel2 = new JPanel(new BorderLayout());
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890 panel2.add(desclabel, BorderLayout.WEST);
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891 panel2.add(description, BorderLayout.CENTER);
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892 panel.add(panel2, BorderLayout.SOUTH);
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895 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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896 panel, "Edit Sequence Name/Description",
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897 JOptionPane.OK_CANCEL_OPTION );
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900 if (reply != JOptionPane.OK_OPTION )
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905 String s = id.getText();
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909 if (s.indexOf(" ") > -1)
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911 JOptionPane.showMessageDialog(ap,
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912 "Spaces have been converted to \"_\"",
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913 "No spaces allowed in Sequence Name",
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914 JOptionPane.WARNING_MESSAGE);
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917 s = s.replace(' ', '_');
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918 sequence.getDatasetSequence().setName(s);
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919 sequence.setName(s);
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923 sequence.getDatasetSequence().setDescription(description.getText());
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924 sequence.setDescription(description.getText());
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930 * @param e DOCUMENT ME!
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932 void unGroupMenuItem_actionPerformed(ActionEvent e)
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934 SequenceGroup sg = ap.av.getSelectionGroup();
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935 ap.av.alignment.deleteGroup(sg);
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936 ap.av.setSelectionGroup(null);
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944 * @param e DOCUMENT ME!
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946 protected void outline_actionPerformed(ActionEvent e)
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948 SequenceGroup sg = getGroup();
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949 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
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954 sg.setOutlineColour(col);
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963 * @param e DOCUMENT ME!
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965 public void showBoxes_actionPerformed(ActionEvent e)
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967 getGroup().setDisplayBoxes(showBoxes.isSelected());
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974 * @param e DOCUMENT ME!
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976 public void showText_actionPerformed(ActionEvent e)
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978 getGroup().setDisplayText(showText.isSelected());
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985 * @param e DOCUMENT ME!
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987 public void showColourText_actionPerformed(ActionEvent e)
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989 getGroup().setColourText(showColourText.isSelected());
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993 public void showLink(String url)
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997 jalview.util.BrowserLauncher.openURL(url);
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999 catch (Exception ex)
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1001 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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1002 "Unixers: Couldn't find default web browser."
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1003 +"\nAdd the full path to your browser in Preferences.",
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1004 "Web browser not found", JOptionPane.WARNING_MESSAGE );
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1007 ex.printStackTrace();
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1011 void hideSequences(boolean representGroup)
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1013 SequenceGroup sg = ap.av.getSelectionGroup();
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1014 if(sg==null || sg.getSize()<1)
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1016 ap.av.hideSequence(sequence);
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1021 while(index < sg.sequences.size())
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1023 if(representGroup && sg.getSequenceAt(index)!=sequence)
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1025 sequence.addHiddenSequence(sg.getSequenceAt(index));
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1026 ap.av.hideSequence(sg.getSequenceAt(index));
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1028 else if(!representGroup)
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1030 ap.av.hideSequence(sg.getSequenceAt(index));
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1035 ap.av.setSelectionGroup(null);
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1039 public void copy_actionPerformed(ActionEvent e)
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1041 ap.alignFrame.copy_actionPerformed(null);
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1044 public void cut_actionPerformed(ActionEvent e)
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1046 ap.alignFrame.cut_actionPerformed(null);
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1049 public void upperCase_actionPerformed(ActionEvent e)
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1051 SequenceGroup sg = ap.av.getSelectionGroup();
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1055 for(int g=0; g<sg.getSize(); g++)
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1057 sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
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1062 public void lowerCase_actionPerformed(ActionEvent e)
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1064 SequenceGroup sg = ap.av.getSelectionGroup();
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1068 for(int g=0; g<sg.getSize(); g++)
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1070 sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
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