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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73 * Creates a new PopupMenu object.
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75 * @param ap DOCUMENT ME!
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76 * @param seq DOCUMENT ME!
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78 public PopupMenu(final AlignmentPanel ap, Sequence seq)
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80 ///////////////////////////////////////////////////////////
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81 // If this is activated from the sequence panel, the user may want to
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82 // edit or annotate a particular residue. Therefore display the residue menu
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84 // If from the IDPanel, we must display the sequence menu
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85 //////////////////////////////////////////////////////////
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89 ButtonGroup colours = new ButtonGroup();
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90 colours.add(noColourmenuItem);
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91 colours.add(clustalColour);
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92 colours.add(zappoColour);
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93 colours.add(taylorColour);
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94 colours.add(hydrophobicityColour);
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95 colours.add(helixColour);
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96 colours.add(strandColour);
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97 colours.add(turnColour);
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98 colours.add(buriedColour);
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99 colours.add(abovePIDColour);
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100 colours.add(userDefinedColour);
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101 colours.add(PIDColour);
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102 colours.add(BLOSUM62Colour);
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108 catch (Exception e)
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110 e.printStackTrace();
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115 && seq.getDatasetSequence().getPDBId() != null)
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117 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements();
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118 while(e.hasMoreElements())
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120 final PDBEntry pdb = (PDBEntry)e.nextElement();
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122 JMenuItem pdbMenuItem = new JMenuItem();
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123 pdbMenuItem.setText("View PDB entry: "+pdb.getId());
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124 pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
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126 public void actionPerformed(ActionEvent e)
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128 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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131 sequenceMenu.add(pdbMenuItem);
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136 SequenceGroup sg = ap.av.getSelectionGroup();
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140 groupName.setText(sg.getName());
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142 if (sg.cs instanceof ZappoColourScheme)
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144 zappoColour.setSelected(true);
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146 else if (sg.cs instanceof TaylorColourScheme)
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148 taylorColour.setSelected(true);
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150 else if (sg.cs instanceof PIDColourScheme)
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152 PIDColour.setSelected(true);
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154 else if (sg.cs instanceof Blosum62ColourScheme)
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156 BLOSUM62Colour.setSelected(true);
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158 else if (sg.cs instanceof UserColourScheme)
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160 userDefinedColour.setSelected(true);
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162 else if (sg.cs instanceof HydrophobicColourScheme)
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164 hydrophobicityColour.setSelected(true);
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166 else if (sg.cs instanceof HelixColourScheme)
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168 helixColour.setSelected(true);
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170 else if (sg.cs instanceof StrandColourScheme)
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172 strandColour.setSelected(true);
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174 else if (sg.cs instanceof TurnColourScheme)
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176 turnColour.setSelected(true);
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178 else if (sg.cs instanceof BuriedColourScheme)
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180 buriedColour.setSelected(true);
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182 else if (sg.cs instanceof ClustalxColourScheme)
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184 clustalColour.setSelected(true);
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188 noColourmenuItem.setSelected(true);
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191 if (sg.cs!=null && sg.cs.conservationApplied())
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193 conservationMenuItem.setSelected(true);
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196 showText.setSelected(sg.getDisplayText());
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197 showColourText.setSelected(sg.getColourText());
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198 showBoxes.setSelected(sg.getDisplayBoxes());
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201 if (!ap.av.alignment.getGroups().contains(sg))
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203 unGroupMenuItem.setVisible(false);
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207 groupMenu.insertSeparator(3);
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212 sequenceMenu.setVisible(false);
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216 java.util.Vector links = Preferences.sequenceURLLinks;
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218 JMenu linkMenu = new JMenu("Link");
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220 for(int i=0; i<links.size(); i++)
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222 String link = links.elementAt(i).toString();
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224 item = new JMenuItem(link.substring(0, link.indexOf("|")));
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225 String id = sequence.getName();
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226 if(id.indexOf("|")>-1)
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227 id = id.substring(id.lastIndexOf("|")+1);
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229 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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231 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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234 item.addActionListener(new java.awt.event.ActionListener()
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236 public void actionPerformed(ActionEvent e)
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242 linkMenu.add(item);
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251 * @throws Exception DOCUMENT ME!
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253 private void jbInit() throws Exception
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255 groupMenu.setText("Group");
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256 groupMenu.setText("Define");
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257 groupName.setText("Name");
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258 groupName.addActionListener(new java.awt.event.ActionListener()
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260 public void actionPerformed(ActionEvent e)
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262 groupName_actionPerformed(e);
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265 sequenceMenu.setText("Sequence");
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266 sequenceName.setText("Edit name");
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267 sequenceName.addActionListener(new java.awt.event.ActionListener()
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269 public void actionPerformed(ActionEvent e)
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271 sequenceName_actionPerformed(e);
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274 PIDColour.setFocusPainted(false);
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275 unGroupMenuItem.setText("Remove Group");
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276 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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278 public void actionPerformed(ActionEvent e)
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280 unGroupMenuItem_actionPerformed(e);
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284 outline.setText("Border colour");
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285 outline.addActionListener(new java.awt.event.ActionListener()
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287 public void actionPerformed(ActionEvent e)
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289 outline_actionPerformed(e);
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292 nucleotideMenuItem.setText("Nucleotide");
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293 nucleotideMenuItem.addActionListener(new ActionListener()
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295 public void actionPerformed(ActionEvent e)
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297 nucleotideMenuItem_actionPerformed(e);
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300 colourMenu.setText("Group Colour");
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301 showBoxes.setText("Boxes");
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302 showBoxes.setState(true);
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303 showBoxes.addActionListener(new ActionListener()
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305 public void actionPerformed(ActionEvent e)
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307 showBoxes_actionPerformed(e);
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310 showText.setText("Text");
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311 showText.setState(true);
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312 showText.addActionListener(new ActionListener()
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314 public void actionPerformed(ActionEvent e)
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316 showText_actionPerformed(e);
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319 showColourText.setText("Colour Text");
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320 showColourText.addActionListener(new ActionListener()
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322 public void actionPerformed(ActionEvent e)
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324 showColourText_actionPerformed(e);
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329 groupMenu.add(groupName);
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330 groupMenu.addSeparator();
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331 groupMenu.add(unGroupMenuItem);
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332 groupMenu.add(colourMenu);
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333 groupMenu.addSeparator();
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334 groupMenu.add(showBoxes);
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335 groupMenu.add(showText);
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336 groupMenu.add(showColourText);
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337 groupMenu.addSeparator();
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338 groupMenu.add(outline);
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339 sequenceMenu.add(sequenceName);
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340 colourMenu.add(noColourmenuItem);
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341 colourMenu.add(clustalColour);
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342 colourMenu.add(BLOSUM62Colour);
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343 colourMenu.add(PIDColour);
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344 colourMenu.add(zappoColour);
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345 colourMenu.add(taylorColour);
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346 colourMenu.add(hydrophobicityColour);
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347 colourMenu.add(helixColour);
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348 colourMenu.add(strandColour);
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349 colourMenu.add(turnColour);
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350 colourMenu.add(buriedColour);
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351 colourMenu.add(nucleotideMenuItem);
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352 colourMenu.add(userDefinedColour);
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354 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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356 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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357 getUserColourSchemes().keys();
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359 while (userColours.hasMoreElements())
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361 JMenuItem item = new JMenuItem(userColours.
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362 nextElement().toString());
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363 item.addActionListener(new ActionListener()
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365 public void actionPerformed(ActionEvent evt)
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367 userDefinedColour_actionPerformed(evt);
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370 colourMenu.add(item);
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375 colourMenu.addSeparator();
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376 colourMenu.add(abovePIDColour);
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377 colourMenu.add(conservationMenuItem);
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378 noColourmenuItem.setText("None");
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379 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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381 public void actionPerformed(ActionEvent e)
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383 noColourmenuItem_actionPerformed(e);
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387 clustalColour.setText("Clustalx colours");
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388 clustalColour.addActionListener(new java.awt.event.ActionListener()
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390 public void actionPerformed(ActionEvent e)
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392 clustalColour_actionPerformed(e);
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395 zappoColour.setText("Zappo");
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396 zappoColour.addActionListener(new java.awt.event.ActionListener()
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398 public void actionPerformed(ActionEvent e)
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400 zappoColour_actionPerformed(e);
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403 taylorColour.setText("Taylor");
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404 taylorColour.addActionListener(new java.awt.event.ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 taylorColour_actionPerformed(e);
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411 hydrophobicityColour.setText("Hydrophobicity");
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412 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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414 public void actionPerformed(ActionEvent e)
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416 hydrophobicityColour_actionPerformed(e);
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419 helixColour.setText("Helix propensity");
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420 helixColour.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 helixColour_actionPerformed(e);
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427 strandColour.setText("Strand propensity");
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428 strandColour.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 strandColour_actionPerformed(e);
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435 turnColour.setText("Turn propensity");
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436 turnColour.addActionListener(new java.awt.event.ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 turnColour_actionPerformed(e);
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443 buriedColour.setText("Buried Index");
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444 buriedColour.addActionListener(new java.awt.event.ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 buriedColour_actionPerformed(e);
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451 abovePIDColour.setText("Above % Identity");
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452 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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454 public void actionPerformed(ActionEvent e)
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456 abovePIDColour_actionPerformed(e);
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459 userDefinedColour.setText("User Defined...");
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460 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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462 public void actionPerformed(ActionEvent e)
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464 userDefinedColour_actionPerformed(e);
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467 PIDColour.setText("Percentage Identity");
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468 PIDColour.addActionListener(new java.awt.event.ActionListener()
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470 public void actionPerformed(ActionEvent e)
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472 PIDColour_actionPerformed(e);
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475 BLOSUM62Colour.setText("BLOSUM62");
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476 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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478 public void actionPerformed(ActionEvent e)
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480 BLOSUM62Colour_actionPerformed(e);
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483 conservationMenuItem.setText("Conservation");
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484 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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486 public void actionPerformed(ActionEvent e)
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488 conservationMenuItem_actionPerformed(e);
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498 SequenceGroup sg = getGroup();
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501 SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
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503 if (superG != null)
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505 superG.setSuperGroupProperties(sg);
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508 if (ap.overviewPanel != null)
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509 ap.overviewPanel.updateOverviewImage();
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511 ap.seqPanel.repaint();
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517 * @param e DOCUMENT ME!
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519 protected void clustalColour_actionPerformed(ActionEvent e)
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521 SequenceGroup sg = getGroup();
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522 sg.cs = new ClustalxColourScheme(sg.sequences,
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523 ap.av.alignment.getWidth());
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530 * @param e DOCUMENT ME!
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532 protected void zappoColour_actionPerformed(ActionEvent e)
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534 getGroup().cs = new ZappoColourScheme();
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541 * @param e DOCUMENT ME!
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543 protected void taylorColour_actionPerformed(ActionEvent e)
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545 getGroup().cs = new TaylorColourScheme();
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552 * @param e DOCUMENT ME!
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554 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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556 getGroup().cs = new HydrophobicColourScheme();
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563 * @param e DOCUMENT ME!
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565 protected void helixColour_actionPerformed(ActionEvent e)
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567 getGroup().cs = new HelixColourScheme();
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574 * @param e DOCUMENT ME!
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576 protected void strandColour_actionPerformed(ActionEvent e)
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578 getGroup().cs = new StrandColourScheme();
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585 * @param e DOCUMENT ME!
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587 protected void turnColour_actionPerformed(ActionEvent e)
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589 getGroup().cs = new TurnColourScheme();
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596 * @param e DOCUMENT ME!
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598 protected void buriedColour_actionPerformed(ActionEvent e)
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600 getGroup().cs = new BuriedColourScheme();
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607 * @param e DOCUMENT ME!
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609 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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611 getGroup().cs = new NucleotideColourScheme();
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618 * @param e DOCUMENT ME!
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620 protected void abovePIDColour_actionPerformed(ActionEvent e)
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622 SequenceGroup sg = getGroup();
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626 if (abovePIDColour.isSelected())
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628 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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629 ap.av.alignment.getWidth()));
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631 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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632 getGroup().getName());
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634 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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636 SliderPanel.showPIDSlider();
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638 else // remove PIDColouring
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640 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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649 * @param e DOCUMENT ME!
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651 protected void userDefinedColour_actionPerformed(ActionEvent e)
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653 SequenceGroup sg = getGroup();
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655 if (e.getActionCommand().equals("User Defined..."))
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656 new UserDefinedColours(ap, sg);
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659 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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660 getUserColourSchemes().get(e.getActionCommand());
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668 * @param e DOCUMENT ME!
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670 protected void PIDColour_actionPerformed(ActionEvent e)
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672 SequenceGroup sg = getGroup();
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673 sg.cs = new PIDColourScheme();
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674 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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675 ap.av.alignment.getWidth()));
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682 * @param e DOCUMENT ME!
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684 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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686 SequenceGroup sg = getGroup();
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688 sg.cs = new Blosum62ColourScheme();
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690 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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691 ap.av.alignment.getWidth()));
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699 * @param e DOCUMENT ME!
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701 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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703 getGroup().cs = null;
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710 * @param e DOCUMENT ME!
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712 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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714 SequenceGroup sg = getGroup();
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718 if (conservationMenuItem.isSelected())
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720 Conservation c = new Conservation("Group",
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721 ResidueProperties.propHash, 3, sg.sequences, 0,
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722 ap.av.alignment.getWidth());
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725 c.verdict(false, ap.av.ConsPercGaps);
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727 sg.cs.setConservation(c);
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729 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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730 SliderPanel.showConservationSlider();
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732 else // remove ConservationColouring
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734 sg.cs.setConservation(null);
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743 * @param e DOCUMENT ME!
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745 protected void groupName_actionPerformed(ActionEvent e)
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747 SequenceGroup sg = getGroup();
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748 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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749 "Enter new group name", "Edit group name",
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750 JOptionPane.QUESTION_MESSAGE);
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758 groupName.setText(reply);
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764 * @param e DOCUMENT ME!
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766 protected void analyze_actionPerformed(ActionEvent e)
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768 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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769 JInternalFrame frame = new JInternalFrame();
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770 frame.setContentPane(cap);
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771 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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773 SequenceGroup sg = getGroup();
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774 StringBuffer sb = new StringBuffer();
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776 for (int i = 0; i < sg.sequences.size(); i++)
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778 Sequence tmp = (Sequence) sg.sequences.get(i);
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779 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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783 sb.append("Something amazing will happen soon");
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784 cap.setText(sb.toString());
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790 * @return DOCUMENT ME!
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792 SequenceGroup getGroup()
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794 SequenceGroup sg = ap.av.getSelectionGroup();
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795 // this method won't add a new group if it already exists
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797 ap.av.alignment.addGroup(sg);
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805 * @param e DOCUMENT ME!
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807 void sequenceName_actionPerformed(ActionEvent e)
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809 String id = sequence.getName();
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810 String s = (String) JOptionPane.showInternalInputDialog(ap,
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811 "Edit sequence name",
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812 "Edit sequence name (" + sequence.getName() + ")",
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813 JOptionPane.PLAIN_MESSAGE, null, null, id);
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817 if (s.indexOf(" ") > -1)
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819 JOptionPane.showMessageDialog(ap,
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820 "Spaces have been converted to \"_\"",
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821 "No spaces allowed in Sequence Name",
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822 JOptionPane.WARNING_MESSAGE);
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825 s = s.replace(' ', '_');
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826 sequence.setName(s);
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834 * @param e DOCUMENT ME!
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836 void unGroupMenuItem_actionPerformed(ActionEvent e)
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838 SequenceGroup sg = ap.av.getSelectionGroup();
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839 ap.av.alignment.deleteGroup(sg);
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840 ap.av.setSelectionGroup(null);
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848 * @param e DOCUMENT ME!
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850 protected void outline_actionPerformed(ActionEvent e)
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852 SequenceGroup sg = getGroup();
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853 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
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858 sg.setOutlineColour(col);
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867 * @param e DOCUMENT ME!
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869 public void showBoxes_actionPerformed(ActionEvent e)
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871 getGroup().setDisplayBoxes(showBoxes.isSelected());
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878 * @param e DOCUMENT ME!
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880 public void showText_actionPerformed(ActionEvent e)
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882 getGroup().setDisplayText(showText.isSelected());
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889 * @param e DOCUMENT ME!
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891 public void showColourText_actionPerformed(ActionEvent e)
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893 getGroup().setColourText(showColourText.isSelected());
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897 public void showLink(String url)
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901 jalview.util.BrowserLauncher.openURL(url);
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903 catch (Exception ex)
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905 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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906 "Unixers: Couldn't find default web browser."
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907 +"\nAdd the full path to your browser in Preferences.",
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908 "Web browser not found", JOptionPane.WARNING_MESSAGE );
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911 ex.printStackTrace();
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