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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76 JMenuItem toggle = new JMenuItem();
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79 * Creates a new PopupMenu object.
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81 * @param ap DOCUMENT ME!
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82 * @param seq DOCUMENT ME!
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84 public PopupMenu(final AlignmentPanel ap, Sequence seq)
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86 ///////////////////////////////////////////////////////////
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87 // If this is activated from the sequence panel, the user may want to
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88 // edit or annotate a particular residue. Therefore display the residue menu
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90 // If from the IDPanel, we must display the sequence menu
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91 //////////////////////////////////////////////////////////
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95 ButtonGroup colours = new ButtonGroup();
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96 colours.add(noColourmenuItem);
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97 colours.add(clustalColour);
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98 colours.add(zappoColour);
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99 colours.add(taylorColour);
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100 colours.add(hydrophobicityColour);
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101 colours.add(helixColour);
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102 colours.add(strandColour);
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103 colours.add(turnColour);
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104 colours.add(buriedColour);
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105 colours.add(abovePIDColour);
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106 colours.add(userDefinedColour);
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107 colours.add(PIDColour);
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108 colours.add(BLOSUM62Colour);
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114 catch (Exception e)
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116 e.printStackTrace();
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122 JMenuItem menuItem;
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123 if( seq.getDatasetSequence().getPDBId() != null)
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125 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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127 while (e.hasMoreElements())
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129 final PDBEntry pdb = (PDBEntry) e.nextElement();
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131 menuItem = new JMenuItem();
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132 menuItem.setText("View PDB entry: " + pdb.getId());
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133 menuItem.addActionListener(new java.awt.event.ActionListener()
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135 public void actionPerformed(ActionEvent e)
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137 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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140 sequenceMenu.add(menuItem);
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144 /* menuItem = new JMenuItem("Hide Sequences");
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145 menuItem.addActionListener(new java.awt.event.ActionListener()
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147 public void actionPerformed(ActionEvent e)
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149 hideSequences(false);
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152 sequenceMenu.add(menuItem);
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154 if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)
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156 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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157 menuItem.addActionListener(new java.awt.event.ActionListener()
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159 public void actionPerformed(ActionEvent e)
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161 hideSequences(true);
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164 sequenceMenu.add(menuItem);
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172 SequenceGroup sg = ap.av.getSelectionGroup();
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176 groupName.setText(sg.getName());
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178 if (sg.cs instanceof ZappoColourScheme)
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180 zappoColour.setSelected(true);
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182 else if (sg.cs instanceof TaylorColourScheme)
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184 taylorColour.setSelected(true);
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186 else if (sg.cs instanceof PIDColourScheme)
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188 PIDColour.setSelected(true);
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190 else if (sg.cs instanceof Blosum62ColourScheme)
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192 BLOSUM62Colour.setSelected(true);
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194 else if (sg.cs instanceof UserColourScheme)
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196 userDefinedColour.setSelected(true);
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198 else if (sg.cs instanceof HydrophobicColourScheme)
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200 hydrophobicityColour.setSelected(true);
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202 else if (sg.cs instanceof HelixColourScheme)
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204 helixColour.setSelected(true);
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206 else if (sg.cs instanceof StrandColourScheme)
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208 strandColour.setSelected(true);
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210 else if (sg.cs instanceof TurnColourScheme)
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212 turnColour.setSelected(true);
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214 else if (sg.cs instanceof BuriedColourScheme)
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216 buriedColour.setSelected(true);
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218 else if (sg.cs instanceof ClustalxColourScheme)
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220 clustalColour.setSelected(true);
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224 noColourmenuItem.setSelected(true);
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227 if (sg.cs!=null && sg.cs.conservationApplied())
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229 conservationMenuItem.setSelected(true);
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232 showText.setSelected(sg.getDisplayText());
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233 showColourText.setSelected(sg.getColourText());
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234 showBoxes.setSelected(sg.getDisplayBoxes());
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238 groupMenu.setVisible(false);
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239 editMenu.setVisible(false);
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242 if (!ap.av.alignment.getGroups().contains(sg))
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244 unGroupMenuItem.setVisible(false);
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248 groupMenu.insertSeparator(3);
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253 sequenceMenu.setVisible(false);
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257 java.util.Vector links = Preferences.sequenceURLLinks;
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259 JMenu linkMenu = new JMenu("Link");
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261 for(int i=0; i<links.size(); i++)
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263 String link = links.elementAt(i).toString();
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265 item = new JMenuItem(link.substring(0, link.indexOf("|")));
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266 String id = sequence.getName();
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267 if(id.indexOf("|")>-1)
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268 id = id.substring(id.lastIndexOf("|")+1);
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270 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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272 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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275 item.addActionListener(new java.awt.event.ActionListener()
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277 public void actionPerformed(ActionEvent e)
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283 linkMenu.add(item);
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293 * @throws Exception DOCUMENT ME!
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295 private void jbInit() throws Exception
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297 groupMenu.setText("Group");
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298 groupMenu.setText("Group");
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299 groupName.setText("Name");
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300 groupName.addActionListener(new java.awt.event.ActionListener()
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302 public void actionPerformed(ActionEvent e)
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304 groupName_actionPerformed(e);
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307 sequenceMenu.setText("Sequence");
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308 sequenceName.setText("Edit Name/Description");
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309 sequenceName.addActionListener(new java.awt.event.ActionListener()
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311 public void actionPerformed(ActionEvent e)
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313 sequenceName_actionPerformed(e);
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316 PIDColour.setFocusPainted(false);
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317 unGroupMenuItem.setText("Remove Group");
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318 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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320 public void actionPerformed(ActionEvent e)
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322 unGroupMenuItem_actionPerformed(e);
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326 outline.setText("Border colour");
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327 outline.addActionListener(new java.awt.event.ActionListener()
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329 public void actionPerformed(ActionEvent e)
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331 outline_actionPerformed(e);
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334 nucleotideMenuItem.setText("Nucleotide");
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335 nucleotideMenuItem.addActionListener(new ActionListener()
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337 public void actionPerformed(ActionEvent e)
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339 nucleotideMenuItem_actionPerformed(e);
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342 colourMenu.setText("Group Colour");
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343 showBoxes.setText("Boxes");
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344 showBoxes.setState(true);
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345 showBoxes.addActionListener(new ActionListener()
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347 public void actionPerformed(ActionEvent e)
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349 showBoxes_actionPerformed(e);
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352 showText.setText("Text");
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353 showText.setState(true);
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354 showText.addActionListener(new ActionListener()
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356 public void actionPerformed(ActionEvent e)
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358 showText_actionPerformed(e);
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361 showColourText.setText("Colour Text");
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362 showColourText.addActionListener(new ActionListener()
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364 public void actionPerformed(ActionEvent e)
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366 showColourText_actionPerformed(e);
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369 editMenu.setText("Edit");
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370 cut.setText("Cut");
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371 cut.addActionListener(new ActionListener()
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373 public void actionPerformed(ActionEvent e)
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375 cut_actionPerformed(e);
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378 upperCase.setText("To Upper Case");
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379 upperCase.addActionListener(new ActionListener()
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381 public void actionPerformed(ActionEvent e)
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383 upperCase_actionPerformed(e);
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386 copy.setText("Copy");
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387 copy.addActionListener(new ActionListener()
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389 public void actionPerformed(ActionEvent e)
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391 copy_actionPerformed(e);
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394 lowerCase.setText("To Lower Case");
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395 lowerCase.addActionListener(new ActionListener()
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397 public void actionPerformed(ActionEvent e)
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399 lowerCase_actionPerformed(e);
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402 toggle.setText("Toggle Case");
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403 toggle.addActionListener(new ActionListener()
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405 public void actionPerformed(ActionEvent e)
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407 toggle_actionPerformed(e);
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412 this.add(editMenu);
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413 groupMenu.add(groupName);
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414 groupMenu.addSeparator();
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415 groupMenu.add(unGroupMenuItem);
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416 groupMenu.add(colourMenu);
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417 groupMenu.addSeparator();
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418 groupMenu.add(showBoxes);
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419 groupMenu.add(showText);
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420 groupMenu.add(showColourText);
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421 groupMenu.addSeparator();
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422 groupMenu.add(outline);
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423 sequenceMenu.add(sequenceName);
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424 colourMenu.add(noColourmenuItem);
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425 colourMenu.add(clustalColour);
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426 colourMenu.add(BLOSUM62Colour);
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427 colourMenu.add(PIDColour);
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428 colourMenu.add(zappoColour);
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429 colourMenu.add(taylorColour);
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430 colourMenu.add(hydrophobicityColour);
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431 colourMenu.add(helixColour);
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432 colourMenu.add(strandColour);
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433 colourMenu.add(turnColour);
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434 colourMenu.add(buriedColour);
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435 colourMenu.add(nucleotideMenuItem);
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436 colourMenu.add(userDefinedColour);
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438 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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440 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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441 getUserColourSchemes().keys();
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443 while (userColours.hasMoreElements())
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445 JMenuItem item = new JMenuItem(userColours.
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446 nextElement().toString());
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447 item.addActionListener(new ActionListener()
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449 public void actionPerformed(ActionEvent evt)
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451 userDefinedColour_actionPerformed(evt);
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454 colourMenu.add(item);
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459 colourMenu.addSeparator();
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460 colourMenu.add(abovePIDColour);
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461 colourMenu.add(conservationMenuItem);
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462 editMenu.add(copy);
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464 editMenu.add(upperCase);
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465 editMenu.add(lowerCase);
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466 editMenu.add(toggle);
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467 noColourmenuItem.setText("None");
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468 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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470 public void actionPerformed(ActionEvent e)
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472 noColourmenuItem_actionPerformed(e);
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476 clustalColour.setText("Clustalx colours");
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477 clustalColour.addActionListener(new java.awt.event.ActionListener()
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479 public void actionPerformed(ActionEvent e)
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481 clustalColour_actionPerformed(e);
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484 zappoColour.setText("Zappo");
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485 zappoColour.addActionListener(new java.awt.event.ActionListener()
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487 public void actionPerformed(ActionEvent e)
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489 zappoColour_actionPerformed(e);
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492 taylorColour.setText("Taylor");
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493 taylorColour.addActionListener(new java.awt.event.ActionListener()
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495 public void actionPerformed(ActionEvent e)
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497 taylorColour_actionPerformed(e);
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500 hydrophobicityColour.setText("Hydrophobicity");
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501 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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503 public void actionPerformed(ActionEvent e)
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505 hydrophobicityColour_actionPerformed(e);
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508 helixColour.setText("Helix propensity");
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509 helixColour.addActionListener(new java.awt.event.ActionListener()
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511 public void actionPerformed(ActionEvent e)
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513 helixColour_actionPerformed(e);
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516 strandColour.setText("Strand propensity");
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517 strandColour.addActionListener(new java.awt.event.ActionListener()
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519 public void actionPerformed(ActionEvent e)
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521 strandColour_actionPerformed(e);
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524 turnColour.setText("Turn propensity");
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525 turnColour.addActionListener(new java.awt.event.ActionListener()
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527 public void actionPerformed(ActionEvent e)
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529 turnColour_actionPerformed(e);
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532 buriedColour.setText("Buried Index");
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533 buriedColour.addActionListener(new java.awt.event.ActionListener()
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535 public void actionPerformed(ActionEvent e)
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537 buriedColour_actionPerformed(e);
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540 abovePIDColour.setText("Above % Identity");
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541 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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543 public void actionPerformed(ActionEvent e)
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545 abovePIDColour_actionPerformed(e);
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548 userDefinedColour.setText("User Defined...");
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549 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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551 public void actionPerformed(ActionEvent e)
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553 userDefinedColour_actionPerformed(e);
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556 PIDColour.setText("Percentage Identity");
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557 PIDColour.addActionListener(new java.awt.event.ActionListener()
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559 public void actionPerformed(ActionEvent e)
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561 PIDColour_actionPerformed(e);
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564 BLOSUM62Colour.setText("BLOSUM62");
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565 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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567 public void actionPerformed(ActionEvent e)
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569 BLOSUM62Colour_actionPerformed(e);
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572 conservationMenuItem.setText("Conservation");
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573 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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575 public void actionPerformed(ActionEvent e)
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577 conservationMenuItem_actionPerformed(e);
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587 if (ap.overviewPanel != null)
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588 ap.overviewPanel.updateOverviewImage();
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590 ap.seqPanel.repaint();
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596 * @param e DOCUMENT ME!
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598 protected void clustalColour_actionPerformed(ActionEvent e)
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600 SequenceGroup sg = getGroup();
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601 sg.cs = new ClustalxColourScheme(sg.sequences,
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602 ap.av.alignment.getWidth());
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609 * @param e DOCUMENT ME!
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611 protected void zappoColour_actionPerformed(ActionEvent e)
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613 getGroup().cs = new ZappoColourScheme();
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620 * @param e DOCUMENT ME!
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622 protected void taylorColour_actionPerformed(ActionEvent e)
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624 getGroup().cs = new TaylorColourScheme();
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631 * @param e DOCUMENT ME!
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633 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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635 getGroup().cs = new HydrophobicColourScheme();
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642 * @param e DOCUMENT ME!
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644 protected void helixColour_actionPerformed(ActionEvent e)
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646 getGroup().cs = new HelixColourScheme();
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653 * @param e DOCUMENT ME!
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655 protected void strandColour_actionPerformed(ActionEvent e)
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657 getGroup().cs = new StrandColourScheme();
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664 * @param e DOCUMENT ME!
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666 protected void turnColour_actionPerformed(ActionEvent e)
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668 getGroup().cs = new TurnColourScheme();
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675 * @param e DOCUMENT ME!
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677 protected void buriedColour_actionPerformed(ActionEvent e)
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679 getGroup().cs = new BuriedColourScheme();
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686 * @param e DOCUMENT ME!
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688 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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690 getGroup().cs = new NucleotideColourScheme();
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697 * @param e DOCUMENT ME!
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699 protected void abovePIDColour_actionPerformed(ActionEvent e)
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701 SequenceGroup sg = getGroup();
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705 if (abovePIDColour.isSelected())
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707 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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708 ap.av.alignment.getWidth()));
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710 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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711 getGroup().getName());
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713 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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715 SliderPanel.showPIDSlider();
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717 else // remove PIDColouring
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719 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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728 * @param e DOCUMENT ME!
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730 protected void userDefinedColour_actionPerformed(ActionEvent e)
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732 SequenceGroup sg = getGroup();
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734 if (e.getActionCommand().equals("User Defined..."))
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735 new UserDefinedColours(ap, sg);
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738 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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739 getUserColourSchemes().get(e.getActionCommand());
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747 * @param e DOCUMENT ME!
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749 protected void PIDColour_actionPerformed(ActionEvent e)
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751 SequenceGroup sg = getGroup();
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752 sg.cs = new PIDColourScheme();
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753 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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754 ap.av.alignment.getWidth()));
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761 * @param e DOCUMENT ME!
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763 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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765 SequenceGroup sg = getGroup();
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767 sg.cs = new Blosum62ColourScheme();
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769 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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770 ap.av.alignment.getWidth()));
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778 * @param e DOCUMENT ME!
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780 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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782 getGroup().cs = null;
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789 * @param e DOCUMENT ME!
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791 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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793 SequenceGroup sg = getGroup();
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797 if (conservationMenuItem.isSelected())
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799 Conservation c = new Conservation("Group",
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800 ResidueProperties.propHash, 3, sg.sequences, 0,
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801 ap.av.alignment.getWidth());
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804 c.verdict(false, ap.av.ConsPercGaps);
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806 sg.cs.setConservation(c);
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808 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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809 SliderPanel.showConservationSlider();
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811 else // remove ConservationColouring
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813 sg.cs.setConservation(null);
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822 * @param e DOCUMENT ME!
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824 protected void groupName_actionPerformed(ActionEvent e)
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826 SequenceGroup sg = getGroup();
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827 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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828 "Enter new group name", "Edit group name",
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829 JOptionPane.QUESTION_MESSAGE);
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837 groupName.setText(reply);
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843 * @param e DOCUMENT ME!
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845 protected void analyze_actionPerformed(ActionEvent e)
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847 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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848 JInternalFrame frame = new JInternalFrame();
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849 frame.setContentPane(cap);
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850 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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852 SequenceGroup sg = getGroup();
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853 StringBuffer sb = new StringBuffer();
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855 for (int i = 0; i < sg.sequences.size(); i++)
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857 Sequence tmp = (Sequence) sg.sequences.get(i);
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858 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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862 sb.append("Something amazing will happen soon");
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863 cap.setText(sb.toString());
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869 * @return DOCUMENT ME!
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871 SequenceGroup getGroup()
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873 SequenceGroup sg = ap.av.getSelectionGroup();
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874 // this method won't add a new group if it already exists
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876 ap.av.alignment.addGroup(sg);
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884 * @param e DOCUMENT ME!
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886 void sequenceName_actionPerformed(ActionEvent e)
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888 JLabel idlabel = new JLabel( " Sequence Name ");
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889 JLabel desclabel = new JLabel("Sequence Description ");
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890 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
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891 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
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892 JTextField id = new JTextField(sequence.getName(), 40);
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893 JTextField description = new JTextField(sequence.getDescription(), 40);
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894 JPanel panel = new JPanel(new BorderLayout());
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895 JPanel panel2 = new JPanel(new BorderLayout());
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896 panel2.add(idlabel, BorderLayout.WEST);
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897 panel2.add(id, BorderLayout.CENTER);
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898 panel.add(panel2, BorderLayout.NORTH);
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899 panel2 = new JPanel(new BorderLayout());
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900 panel2.add(desclabel, BorderLayout.WEST);
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901 panel2.add(description, BorderLayout.CENTER);
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902 panel.add(panel2, BorderLayout.SOUTH);
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905 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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906 panel, "Edit Sequence Name/Description",
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907 JOptionPane.OK_CANCEL_OPTION );
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910 if (reply != JOptionPane.OK_OPTION )
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915 String s = id.getText();
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919 if (s.indexOf(" ") > -1)
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921 JOptionPane.showMessageDialog(ap,
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922 "Spaces have been converted to \"_\"",
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923 "No spaces allowed in Sequence Name",
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924 JOptionPane.WARNING_MESSAGE);
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927 s = s.replace(' ', '_');
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928 sequence.getDatasetSequence().setName(s);
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929 sequence.setName(s);
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933 sequence.getDatasetSequence().setDescription(description.getText());
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934 sequence.setDescription(description.getText());
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940 * @param e DOCUMENT ME!
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942 void unGroupMenuItem_actionPerformed(ActionEvent e)
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944 SequenceGroup sg = ap.av.getSelectionGroup();
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945 ap.av.alignment.deleteGroup(sg);
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946 ap.av.setSelectionGroup(null);
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954 * @param e DOCUMENT ME!
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956 protected void outline_actionPerformed(ActionEvent e)
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958 SequenceGroup sg = getGroup();
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959 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
964 sg.setOutlineColour(col);
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973 * @param e DOCUMENT ME!
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975 public void showBoxes_actionPerformed(ActionEvent e)
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977 getGroup().setDisplayBoxes(showBoxes.isSelected());
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984 * @param e DOCUMENT ME!
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986 public void showText_actionPerformed(ActionEvent e)
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988 getGroup().setDisplayText(showText.isSelected());
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995 * @param e DOCUMENT ME!
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997 public void showColourText_actionPerformed(ActionEvent e)
\r
999 getGroup().setColourText(showColourText.isSelected());
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1003 public void showLink(String url)
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1007 jalview.util.BrowserLauncher.openURL(url);
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1009 catch (Exception ex)
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1011 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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1012 "Unixers: Couldn't find default web browser."
\r
1013 +"\nAdd the full path to your browser in Preferences.",
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1014 "Web browser not found", JOptionPane.WARNING_MESSAGE );
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1017 ex.printStackTrace();
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1021 void hideSequences(boolean representGroup)
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1023 SequenceGroup sg = ap.av.getSelectionGroup();
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1024 if(sg==null || sg.getSize()<1)
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1026 ap.av.hideSequence(sequence);
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1031 while(index < sg.sequences.size())
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1033 if(representGroup && sg.getSequenceAt(index)!=sequence)
\r
1035 sequence.addHiddenSequence(sg.getSequenceAt(index));
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1036 ap.av.hideSequence(sg.getSequenceAt(index));
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1038 else if(!representGroup)
\r
1040 ap.av.hideSequence(sg.getSequenceAt(index));
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1045 ap.av.setSelectionGroup(null);
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1049 public void copy_actionPerformed(ActionEvent e)
\r
1051 ap.alignFrame.copy_actionPerformed(null);
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1054 public void cut_actionPerformed(ActionEvent e)
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1056 ap.alignFrame.cut_actionPerformed(null);
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1059 public void upperCase_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++)
\r
1067 sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
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1072 public void lowerCase_actionPerformed(ActionEvent e)
\r
1074 SequenceGroup sg = ap.av.getSelectionGroup();
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1078 for(int g=0; g<sg.getSize(); g++)
\r
1080 sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
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1085 public void toggle_actionPerformed(ActionEvent e)
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1087 SequenceGroup sg = ap.av.getSelectionGroup();
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1091 for (int g = 0; g < sg.getSize(); g++)
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1093 sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
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