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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116 JMenuItem menuItem;
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117 if( seq.getDatasetSequence().getPDBId() != null)
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119 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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121 while (e.hasMoreElements())
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123 final PDBEntry pdb = (PDBEntry) e.nextElement();
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125 menuItem = new JMenuItem();
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126 menuItem.setText("View PDB entry: " + pdb.getId());
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127 menuItem.addActionListener(new java.awt.event.ActionListener()
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129 public void actionPerformed(ActionEvent e)
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131 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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134 sequenceMenu.add(menuItem);
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138 menuItem = new JMenuItem("Hide Sequences");
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139 menuItem.addActionListener(new java.awt.event.ActionListener()
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141 public void actionPerformed(ActionEvent e)
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143 hideSequences(false);
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146 sequenceMenu.add(menuItem);
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148 if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1)
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150 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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151 menuItem.addActionListener(new java.awt.event.ActionListener()
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153 public void actionPerformed(ActionEvent e)
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155 hideSequences(true);
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158 sequenceMenu.add(menuItem);
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166 SequenceGroup sg = ap.av.getSelectionGroup();
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170 groupName.setText(sg.getName());
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172 if (sg.cs instanceof ZappoColourScheme)
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174 zappoColour.setSelected(true);
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176 else if (sg.cs instanceof TaylorColourScheme)
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178 taylorColour.setSelected(true);
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180 else if (sg.cs instanceof PIDColourScheme)
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182 PIDColour.setSelected(true);
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184 else if (sg.cs instanceof Blosum62ColourScheme)
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186 BLOSUM62Colour.setSelected(true);
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188 else if (sg.cs instanceof UserColourScheme)
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190 userDefinedColour.setSelected(true);
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192 else if (sg.cs instanceof HydrophobicColourScheme)
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194 hydrophobicityColour.setSelected(true);
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196 else if (sg.cs instanceof HelixColourScheme)
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198 helixColour.setSelected(true);
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200 else if (sg.cs instanceof StrandColourScheme)
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202 strandColour.setSelected(true);
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204 else if (sg.cs instanceof TurnColourScheme)
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206 turnColour.setSelected(true);
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208 else if (sg.cs instanceof BuriedColourScheme)
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210 buriedColour.setSelected(true);
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212 else if (sg.cs instanceof ClustalxColourScheme)
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214 clustalColour.setSelected(true);
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218 noColourmenuItem.setSelected(true);
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221 if (sg.cs!=null && sg.cs.conservationApplied())
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223 conservationMenuItem.setSelected(true);
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226 showText.setSelected(sg.getDisplayText());
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227 showColourText.setSelected(sg.getColourText());
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228 showBoxes.setSelected(sg.getDisplayBoxes());
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231 if (!ap.av.alignment.getGroups().contains(sg))
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233 unGroupMenuItem.setVisible(false);
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237 groupMenu.insertSeparator(3);
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242 sequenceMenu.setVisible(false);
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246 java.util.Vector links = Preferences.sequenceURLLinks;
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248 JMenu linkMenu = new JMenu("Link");
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250 for(int i=0; i<links.size(); i++)
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252 String link = links.elementAt(i).toString();
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254 item = new JMenuItem(link.substring(0, link.indexOf("|")));
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255 String id = sequence.getName();
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256 if(id.indexOf("|")>-1)
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257 id = id.substring(id.lastIndexOf("|")+1);
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259 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
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261 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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264 item.addActionListener(new java.awt.event.ActionListener()
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266 public void actionPerformed(ActionEvent e)
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272 linkMenu.add(item);
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282 * @throws Exception DOCUMENT ME!
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284 private void jbInit() throws Exception
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286 groupMenu.setText("Group");
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287 groupMenu.setText("Define");
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288 groupName.setText("Name");
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289 groupName.addActionListener(new java.awt.event.ActionListener()
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291 public void actionPerformed(ActionEvent e)
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293 groupName_actionPerformed(e);
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296 sequenceMenu.setText("Sequence");
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297 sequenceName.setText("Edit Name/Desciption");
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298 sequenceName.addActionListener(new java.awt.event.ActionListener()
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300 public void actionPerformed(ActionEvent e)
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302 sequenceName_actionPerformed(e);
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305 PIDColour.setFocusPainted(false);
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306 unGroupMenuItem.setText("Remove Group");
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307 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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309 public void actionPerformed(ActionEvent e)
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311 unGroupMenuItem_actionPerformed(e);
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315 outline.setText("Border colour");
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316 outline.addActionListener(new java.awt.event.ActionListener()
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318 public void actionPerformed(ActionEvent e)
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320 outline_actionPerformed(e);
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323 nucleotideMenuItem.setText("Nucleotide");
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324 nucleotideMenuItem.addActionListener(new ActionListener()
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326 public void actionPerformed(ActionEvent e)
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328 nucleotideMenuItem_actionPerformed(e);
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331 colourMenu.setText("Group Colour");
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332 showBoxes.setText("Boxes");
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333 showBoxes.setState(true);
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334 showBoxes.addActionListener(new ActionListener()
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336 public void actionPerformed(ActionEvent e)
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338 showBoxes_actionPerformed(e);
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341 showText.setText("Text");
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342 showText.setState(true);
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343 showText.addActionListener(new ActionListener()
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345 public void actionPerformed(ActionEvent e)
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347 showText_actionPerformed(e);
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350 showColourText.setText("Colour Text");
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351 showColourText.addActionListener(new ActionListener()
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353 public void actionPerformed(ActionEvent e)
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355 showColourText_actionPerformed(e);
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360 groupMenu.add(groupName);
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361 groupMenu.addSeparator();
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362 groupMenu.add(unGroupMenuItem);
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363 groupMenu.add(colourMenu);
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364 groupMenu.addSeparator();
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365 groupMenu.add(showBoxes);
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366 groupMenu.add(showText);
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367 groupMenu.add(showColourText);
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368 groupMenu.addSeparator();
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369 groupMenu.add(outline);
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370 sequenceMenu.add(sequenceName);
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371 colourMenu.add(noColourmenuItem);
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372 colourMenu.add(clustalColour);
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373 colourMenu.add(BLOSUM62Colour);
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374 colourMenu.add(PIDColour);
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375 colourMenu.add(zappoColour);
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376 colourMenu.add(taylorColour);
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377 colourMenu.add(hydrophobicityColour);
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378 colourMenu.add(helixColour);
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379 colourMenu.add(strandColour);
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380 colourMenu.add(turnColour);
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381 colourMenu.add(buriedColour);
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382 colourMenu.add(nucleotideMenuItem);
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383 colourMenu.add(userDefinedColour);
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385 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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387 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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388 getUserColourSchemes().keys();
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390 while (userColours.hasMoreElements())
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392 JMenuItem item = new JMenuItem(userColours.
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393 nextElement().toString());
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394 item.addActionListener(new ActionListener()
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396 public void actionPerformed(ActionEvent evt)
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398 userDefinedColour_actionPerformed(evt);
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401 colourMenu.add(item);
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406 colourMenu.addSeparator();
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407 colourMenu.add(abovePIDColour);
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408 colourMenu.add(conservationMenuItem);
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409 noColourmenuItem.setText("None");
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410 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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412 public void actionPerformed(ActionEvent e)
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414 noColourmenuItem_actionPerformed(e);
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418 clustalColour.setText("Clustalx colours");
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419 clustalColour.addActionListener(new java.awt.event.ActionListener()
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421 public void actionPerformed(ActionEvent e)
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423 clustalColour_actionPerformed(e);
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426 zappoColour.setText("Zappo");
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427 zappoColour.addActionListener(new java.awt.event.ActionListener()
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429 public void actionPerformed(ActionEvent e)
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431 zappoColour_actionPerformed(e);
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434 taylorColour.setText("Taylor");
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435 taylorColour.addActionListener(new java.awt.event.ActionListener()
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437 public void actionPerformed(ActionEvent e)
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439 taylorColour_actionPerformed(e);
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442 hydrophobicityColour.setText("Hydrophobicity");
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443 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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445 public void actionPerformed(ActionEvent e)
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447 hydrophobicityColour_actionPerformed(e);
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450 helixColour.setText("Helix propensity");
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451 helixColour.addActionListener(new java.awt.event.ActionListener()
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453 public void actionPerformed(ActionEvent e)
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455 helixColour_actionPerformed(e);
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458 strandColour.setText("Strand propensity");
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459 strandColour.addActionListener(new java.awt.event.ActionListener()
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461 public void actionPerformed(ActionEvent e)
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463 strandColour_actionPerformed(e);
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466 turnColour.setText("Turn propensity");
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467 turnColour.addActionListener(new java.awt.event.ActionListener()
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469 public void actionPerformed(ActionEvent e)
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471 turnColour_actionPerformed(e);
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474 buriedColour.setText("Buried Index");
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475 buriedColour.addActionListener(new java.awt.event.ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 buriedColour_actionPerformed(e);
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482 abovePIDColour.setText("Above % Identity");
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483 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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485 public void actionPerformed(ActionEvent e)
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487 abovePIDColour_actionPerformed(e);
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490 userDefinedColour.setText("User Defined...");
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491 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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493 public void actionPerformed(ActionEvent e)
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495 userDefinedColour_actionPerformed(e);
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498 PIDColour.setText("Percentage Identity");
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499 PIDColour.addActionListener(new java.awt.event.ActionListener()
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501 public void actionPerformed(ActionEvent e)
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503 PIDColour_actionPerformed(e);
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506 BLOSUM62Colour.setText("BLOSUM62");
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507 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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509 public void actionPerformed(ActionEvent e)
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511 BLOSUM62Colour_actionPerformed(e);
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514 conservationMenuItem.setText("Conservation");
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515 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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517 public void actionPerformed(ActionEvent e)
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519 conservationMenuItem_actionPerformed(e);
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529 if (ap.overviewPanel != null)
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530 ap.overviewPanel.updateOverviewImage();
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532 ap.seqPanel.repaint();
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538 * @param e DOCUMENT ME!
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540 protected void clustalColour_actionPerformed(ActionEvent e)
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542 SequenceGroup sg = getGroup();
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543 sg.cs = new ClustalxColourScheme(sg.sequences,
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544 ap.av.alignment.getWidth());
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551 * @param e DOCUMENT ME!
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553 protected void zappoColour_actionPerformed(ActionEvent e)
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555 getGroup().cs = new ZappoColourScheme();
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562 * @param e DOCUMENT ME!
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564 protected void taylorColour_actionPerformed(ActionEvent e)
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566 getGroup().cs = new TaylorColourScheme();
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573 * @param e DOCUMENT ME!
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575 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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577 getGroup().cs = new HydrophobicColourScheme();
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584 * @param e DOCUMENT ME!
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586 protected void helixColour_actionPerformed(ActionEvent e)
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588 getGroup().cs = new HelixColourScheme();
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595 * @param e DOCUMENT ME!
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597 protected void strandColour_actionPerformed(ActionEvent e)
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599 getGroup().cs = new StrandColourScheme();
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606 * @param e DOCUMENT ME!
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608 protected void turnColour_actionPerformed(ActionEvent e)
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610 getGroup().cs = new TurnColourScheme();
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617 * @param e DOCUMENT ME!
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619 protected void buriedColour_actionPerformed(ActionEvent e)
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621 getGroup().cs = new BuriedColourScheme();
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628 * @param e DOCUMENT ME!
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630 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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632 getGroup().cs = new NucleotideColourScheme();
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639 * @param e DOCUMENT ME!
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641 protected void abovePIDColour_actionPerformed(ActionEvent e)
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643 SequenceGroup sg = getGroup();
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647 if (abovePIDColour.isSelected())
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649 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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650 ap.av.alignment.getWidth()));
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652 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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653 getGroup().getName());
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655 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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657 SliderPanel.showPIDSlider();
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659 else // remove PIDColouring
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661 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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670 * @param e DOCUMENT ME!
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672 protected void userDefinedColour_actionPerformed(ActionEvent e)
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674 SequenceGroup sg = getGroup();
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676 if (e.getActionCommand().equals("User Defined..."))
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677 new UserDefinedColours(ap, sg);
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680 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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681 getUserColourSchemes().get(e.getActionCommand());
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689 * @param e DOCUMENT ME!
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691 protected void PIDColour_actionPerformed(ActionEvent e)
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693 SequenceGroup sg = getGroup();
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694 sg.cs = new PIDColourScheme();
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695 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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696 ap.av.alignment.getWidth()));
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703 * @param e DOCUMENT ME!
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705 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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707 SequenceGroup sg = getGroup();
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709 sg.cs = new Blosum62ColourScheme();
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711 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
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712 ap.av.alignment.getWidth()));
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720 * @param e DOCUMENT ME!
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722 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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724 getGroup().cs = null;
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731 * @param e DOCUMENT ME!
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733 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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735 SequenceGroup sg = getGroup();
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739 if (conservationMenuItem.isSelected())
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741 Conservation c = new Conservation("Group",
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742 ResidueProperties.propHash, 3, sg.sequences, 0,
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743 ap.av.alignment.getWidth());
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746 c.verdict(false, ap.av.ConsPercGaps);
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748 sg.cs.setConservation(c);
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750 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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751 SliderPanel.showConservationSlider();
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753 else // remove ConservationColouring
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755 sg.cs.setConservation(null);
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764 * @param e DOCUMENT ME!
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766 protected void groupName_actionPerformed(ActionEvent e)
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768 SequenceGroup sg = getGroup();
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769 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
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770 "Enter new group name", "Edit group name",
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771 JOptionPane.QUESTION_MESSAGE);
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779 groupName.setText(reply);
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785 * @param e DOCUMENT ME!
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787 protected void analyze_actionPerformed(ActionEvent e)
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789 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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790 JInternalFrame frame = new JInternalFrame();
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791 frame.setContentPane(cap);
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792 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
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794 SequenceGroup sg = getGroup();
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795 StringBuffer sb = new StringBuffer();
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797 for (int i = 0; i < sg.sequences.size(); i++)
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799 Sequence tmp = (Sequence) sg.sequences.get(i);
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800 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
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804 sb.append("Something amazing will happen soon");
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805 cap.setText(sb.toString());
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811 * @return DOCUMENT ME!
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813 SequenceGroup getGroup()
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815 SequenceGroup sg = ap.av.getSelectionGroup();
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816 // this method won't add a new group if it already exists
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818 ap.av.alignment.addGroup(sg);
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826 * @param e DOCUMENT ME!
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828 void sequenceName_actionPerformed(ActionEvent e)
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830 JLabel idlabel = new JLabel( " Sequence Name ");
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831 JLabel desclabel = new JLabel("Sequence Description ");
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832 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
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833 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
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834 JTextField id = new JTextField(sequence.getName(), 40);
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835 JTextField description = new JTextField(sequence.getDescription(), 40);
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836 JPanel panel = new JPanel(new BorderLayout());
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837 JPanel panel2 = new JPanel(new BorderLayout());
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838 panel2.add(idlabel, BorderLayout.WEST);
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839 panel2.add(id, BorderLayout.CENTER);
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840 panel.add(panel2, BorderLayout.NORTH);
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841 panel2 = new JPanel(new BorderLayout());
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842 panel2.add(desclabel, BorderLayout.WEST);
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843 panel2.add(description, BorderLayout.CENTER);
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844 panel.add(panel2, BorderLayout.SOUTH);
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847 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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848 panel, "Edit Sequence Name/Description",
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849 JOptionPane.OK_CANCEL_OPTION );
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852 if (reply != JOptionPane.OK_OPTION )
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857 String s = id.getText();
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861 if (s.indexOf(" ") > -1)
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863 JOptionPane.showMessageDialog(ap,
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864 "Spaces have been converted to \"_\"",
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865 "No spaces allowed in Sequence Name",
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866 JOptionPane.WARNING_MESSAGE);
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869 s = s.replace(' ', '_');
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870 sequence.getDatasetSequence().setName(s);
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871 sequence.setName(s);
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875 sequence.getDatasetSequence().setDescription(description.getText());
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876 sequence.setDescription(description.getText());
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882 * @param e DOCUMENT ME!
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884 void unGroupMenuItem_actionPerformed(ActionEvent e)
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886 SequenceGroup sg = ap.av.getSelectionGroup();
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887 ap.av.alignment.deleteGroup(sg);
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888 ap.av.setSelectionGroup(null);
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896 * @param e DOCUMENT ME!
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898 protected void outline_actionPerformed(ActionEvent e)
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900 SequenceGroup sg = getGroup();
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901 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
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906 sg.setOutlineColour(col);
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915 * @param e DOCUMENT ME!
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917 public void showBoxes_actionPerformed(ActionEvent e)
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919 getGroup().setDisplayBoxes(showBoxes.isSelected());
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926 * @param e DOCUMENT ME!
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928 public void showText_actionPerformed(ActionEvent e)
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930 getGroup().setDisplayText(showText.isSelected());
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937 * @param e DOCUMENT ME!
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939 public void showColourText_actionPerformed(ActionEvent e)
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941 getGroup().setColourText(showColourText.isSelected());
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945 public void showLink(String url)
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949 jalview.util.BrowserLauncher.openURL(url);
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951 catch (Exception ex)
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953 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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954 "Unixers: Couldn't find default web browser."
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955 +"\nAdd the full path to your browser in Preferences.",
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956 "Web browser not found", JOptionPane.WARNING_MESSAGE );
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959 ex.printStackTrace();
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963 void hideSequences(boolean representGroup)
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965 SequenceGroup sg = ap.av.getSelectionGroup();
\r
966 if(sg==null || sg.getSize()<1)
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968 ap.av.hideSequence(sequence);
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973 while(index < sg.sequences.size())
\r
975 if(representGroup && sg.getSequenceAt(index)!=sequence)
\r
977 sequence.addHiddenSequence(sg.getSequenceAt(index));
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978 ap.av.hideSequence(sg.getSequenceAt(index));
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980 else if(!representGroup)
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982 ap.av.hideSequence(sg.getSequenceAt(index));
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987 ap.av.setSelectionGroup(null);
\r