2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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24 import jalview.datamodel.*;
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25 import jalview.schemes.*;
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26 import jalview.commands.ChangeCaseCommand;
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29 import java.awt.event.*;
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31 import javax.swing.*;
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33 import java.util.Vector;
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34 import jalview.io.FormatAdapter;
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35 import javax.swing.event.ChangeListener;
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36 import javax.swing.event.ChangeEvent;
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43 * @version $Revision$
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45 public class PopupMenu extends JPopupMenu
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47 JMenu groupMenu = new JMenu();
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48 JMenuItem groupName = new JMenuItem();
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49 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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57 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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58 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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61 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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62 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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64 JMenu sequenceMenu = new JMenu();
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65 JMenuItem sequenceName = new JMenuItem();
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67 JMenuItem unGroupMenuItem = new JMenuItem();
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68 JMenuItem outline = new JMenuItem();
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69 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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70 JMenu colourMenu = new JMenu();
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71 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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72 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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73 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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74 JMenu editMenu = new JMenu();
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75 JMenuItem cut = new JMenuItem();
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76 JMenuItem copy = new JMenuItem();
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77 JMenuItem upperCase = new JMenuItem();
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78 JMenuItem lowerCase = new JMenuItem();
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79 JMenuItem toggle = new JMenuItem();
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80 JMenu pdbMenu = new JMenu();
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81 JMenuItem pdbFromFile = new JMenuItem();
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82 JMenuItem enterPDB = new JMenuItem();
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83 JMenuItem discoverPDB = new JMenuItem();
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84 JMenu outputMenu = new JMenu();
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85 JMenuItem sequenceFeature = new JMenuItem();
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86 JMenuItem textColour = new JMenuItem();
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87 JMenu jMenu1 = new JMenu();
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90 * Creates a new PopupMenu object.
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92 * @param ap DOCUMENT ME!
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93 * @param seq DOCUMENT ME!
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95 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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97 ///////////////////////////////////////////////////////////
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98 // If this is activated from the sequence panel, the user may want to
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99 // edit or annotate a particular residue. Therefore display the residue menu
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101 // If from the IDPanel, we must display the sequence menu
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102 //////////////////////////////////////////////////////////
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106 ButtonGroup colours = new ButtonGroup();
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107 colours.add(noColourmenuItem);
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108 colours.add(clustalColour);
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109 colours.add(zappoColour);
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110 colours.add(taylorColour);
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111 colours.add(hydrophobicityColour);
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112 colours.add(helixColour);
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113 colours.add(strandColour);
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114 colours.add(turnColour);
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115 colours.add(buriedColour);
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116 colours.add(abovePIDColour);
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117 colours.add(userDefinedColour);
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118 colours.add(PIDColour);
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119 colours.add(BLOSUM62Colour);
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121 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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123 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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125 item.addActionListener(new java.awt.event.ActionListener()
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127 public void actionPerformed(ActionEvent e)
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129 outputText_actionPerformed(e);
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133 outputMenu.add(item);
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141 catch (Exception e)
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143 e.printStackTrace();
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149 sequenceMenu.setText(sequence.getName());
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151 JMenuItem menuItem;
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152 if( seq.getDatasetSequence().getPDBId() != null)
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154 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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157 while (e.hasMoreElements())
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159 final PDBEntry pdb = (PDBEntry) e.nextElement();
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161 menuItem = new JMenuItem();
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162 menuItem.setText("View PDB entry: " + pdb.getId());
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163 menuItem.addActionListener(new java.awt.event.ActionListener()
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165 public void actionPerformed(ActionEvent e)
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167 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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170 sequenceMenu.add(menuItem);
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174 menuItem = new JMenuItem("Hide Sequences");
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175 menuItem.addActionListener(new java.awt.event.ActionListener()
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177 public void actionPerformed(ActionEvent e)
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179 hideSequences(false);
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184 if(ap.av.getSelectionGroup() !=null
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185 && ap.av.getSelectionGroup().getSize(false)>1)
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187 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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188 menuItem.addActionListener(new java.awt.event.ActionListener()
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190 public void actionPerformed(ActionEvent e)
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192 hideSequences(true);
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195 sequenceMenu.add(menuItem);
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198 if (ap.av.hasHiddenRows)
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200 final int index = ap.av.alignment.findIndex(seq);
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202 if (ap.av.adjustForHiddenSeqs(index) -
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203 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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205 menuItem = new JMenuItem("Reveal Sequences");
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206 menuItem.addActionListener(new ActionListener()
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208 public void actionPerformed(ActionEvent e)
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210 ap.av.showSequence(index);
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211 if (ap.overviewPanel != null)
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212 ap.overviewPanel.updateOverviewImage();
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218 menuItem = new JMenuItem("Reveal All");
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219 menuItem.addActionListener(new ActionListener()
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221 public void actionPerformed(ActionEvent e)
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223 ap.av.showAllHiddenSeqs();
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224 if (ap.overviewPanel != null)
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225 ap.overviewPanel.updateOverviewImage();
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237 SequenceGroup sg = ap.av.getSelectionGroup();
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241 groupName.setText(sg.getName());
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243 if (sg.cs instanceof ZappoColourScheme)
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245 zappoColour.setSelected(true);
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247 else if (sg.cs instanceof TaylorColourScheme)
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249 taylorColour.setSelected(true);
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251 else if (sg.cs instanceof PIDColourScheme)
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253 PIDColour.setSelected(true);
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255 else if (sg.cs instanceof Blosum62ColourScheme)
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257 BLOSUM62Colour.setSelected(true);
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259 else if (sg.cs instanceof UserColourScheme)
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261 userDefinedColour.setSelected(true);
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263 else if (sg.cs instanceof HydrophobicColourScheme)
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265 hydrophobicityColour.setSelected(true);
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267 else if (sg.cs instanceof HelixColourScheme)
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269 helixColour.setSelected(true);
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271 else if (sg.cs instanceof StrandColourScheme)
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273 strandColour.setSelected(true);
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275 else if (sg.cs instanceof TurnColourScheme)
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277 turnColour.setSelected(true);
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279 else if (sg.cs instanceof BuriedColourScheme)
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281 buriedColour.setSelected(true);
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283 else if (sg.cs instanceof ClustalxColourScheme)
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285 clustalColour.setSelected(true);
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289 noColourmenuItem.setSelected(true);
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292 if (sg.cs!=null && sg.cs.conservationApplied())
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294 conservationMenuItem.setSelected(true);
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297 showText.setSelected(sg.getDisplayText());
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298 showColourText.setSelected(sg.getColourText());
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299 showBoxes.setSelected(sg.getDisplayBoxes());
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303 groupMenu.setVisible(false);
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304 editMenu.setVisible(false);
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307 if (!ap.av.alignment.getGroups().contains(sg))
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309 unGroupMenuItem.setVisible(false);
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315 sequenceMenu.setVisible(false);
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316 pdbMenu.setVisible(false);
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319 if(links != null && links.size()>0)
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321 JMenu linkMenu = new JMenu("Link");
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323 for(int i=0; i<links.size(); i++)
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325 String link = links.elementAt(i).toString();
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326 final String label = link.substring(0, link.indexOf("|"));
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327 item = new JMenuItem(label);
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330 if (link.indexOf("$SEQUENCE_ID$") > -1)
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332 String id = seq.getName();
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333 if (id.indexOf("|") > -1)
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334 id = id.substring(id.lastIndexOf("|") + 1);
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336 url = link.substring(link.indexOf("|") + 1,
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337 link.indexOf("$SEQUENCE_ID$"))
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339 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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342 url = link.substring(link.lastIndexOf("|")+1);
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345 item.addActionListener(new java.awt.event.ActionListener()
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347 public void actionPerformed(ActionEvent e)
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353 linkMenu.add(item);
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356 sequenceMenu.add(linkMenu);
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366 * @throws Exception DOCUMENT ME!
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368 private void jbInit() throws Exception
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370 groupMenu.setText("Group");
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371 groupMenu.setText("Selection");
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372 groupName.setText("Name");
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373 groupName.addActionListener(new java.awt.event.ActionListener()
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375 public void actionPerformed(ActionEvent e)
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377 groupName_actionPerformed(e);
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380 sequenceMenu.setText("Sequence");
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381 sequenceName.setText("Edit Name/Description");
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382 sequenceName.addActionListener(new java.awt.event.ActionListener()
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384 public void actionPerformed(ActionEvent e)
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386 sequenceName_actionPerformed(e);
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389 PIDColour.setFocusPainted(false);
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390 unGroupMenuItem.setText("Remove Group");
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391 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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393 public void actionPerformed(ActionEvent e)
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395 unGroupMenuItem_actionPerformed(e);
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399 outline.setText("Border colour");
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400 outline.addActionListener(new java.awt.event.ActionListener()
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402 public void actionPerformed(ActionEvent e)
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404 outline_actionPerformed(e);
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407 nucleotideMenuItem.setText("Nucleotide");
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408 nucleotideMenuItem.addActionListener(new ActionListener()
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410 public void actionPerformed(ActionEvent e)
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412 nucleotideMenuItem_actionPerformed(e);
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415 colourMenu.setText("Group Colour");
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416 showBoxes.setText("Boxes");
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417 showBoxes.setState(true);
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418 showBoxes.addActionListener(new ActionListener()
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420 public void actionPerformed(ActionEvent e)
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422 showBoxes_actionPerformed(e);
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425 showText.setText("Text");
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426 showText.setState(true);
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427 showText.addActionListener(new ActionListener()
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429 public void actionPerformed(ActionEvent e)
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431 showText_actionPerformed(e);
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434 showColourText.setText("Colour Text");
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435 showColourText.addActionListener(new ActionListener()
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437 public void actionPerformed(ActionEvent e)
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439 showColourText_actionPerformed(e);
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442 editMenu.setText("Edit");
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443 cut.setText("Cut");
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444 cut.addActionListener(new ActionListener()
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446 public void actionPerformed(ActionEvent e)
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448 cut_actionPerformed(e);
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451 upperCase.setText("To Upper Case");
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452 upperCase.addActionListener(new ActionListener()
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454 public void actionPerformed(ActionEvent e)
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459 copy.setText("Copy");
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460 copy.addActionListener(new ActionListener()
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462 public void actionPerformed(ActionEvent e)
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464 copy_actionPerformed(e);
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467 lowerCase.setText("To Lower Case");
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468 lowerCase.addActionListener(new ActionListener()
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470 public void actionPerformed(ActionEvent e)
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475 toggle.setText("Toggle Case");
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476 toggle.addActionListener(new ActionListener()
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478 public void actionPerformed(ActionEvent e)
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483 pdbMenu.setText("Associate Structure with Sequence");
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484 pdbFromFile.setText("From File");
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485 pdbFromFile.addActionListener(new ActionListener()
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487 public void actionPerformed(ActionEvent e)
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489 pdbFromFile_actionPerformed(e);
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492 enterPDB.setText("Enter PDB Id");
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493 enterPDB.addActionListener(new ActionListener()
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495 public void actionPerformed(ActionEvent e)
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497 enterPDB_actionPerformed(e);
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500 discoverPDB.setText("Discover PDB ids");
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501 discoverPDB.addActionListener(new ActionListener()
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503 public void actionPerformed(ActionEvent e)
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505 discoverPDB_actionPerformed(e);
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508 outputMenu.setText("Output to Textbox...");
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509 sequenceFeature.setText("Create Sequence Feature");
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510 sequenceFeature.addActionListener(new ActionListener()
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512 public void actionPerformed(ActionEvent e)
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514 sequenceFeature_actionPerformed(e);
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517 textColour.setText("Text Colour");
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518 textColour.addActionListener(new ActionListener()
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520 public void actionPerformed(ActionEvent e)
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522 textColour_actionPerformed(e);
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525 jMenu1.setText("Group");
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529 groupMenu.add(editMenu);
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530 groupMenu.add(outputMenu);
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531 groupMenu.add(sequenceFeature);
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532 groupMenu.add(jMenu1);
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533 sequenceMenu.add(sequenceName);
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534 sequenceMenu.add(pdbMenu);
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535 colourMenu.add(textColour);
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536 colourMenu.add(noColourmenuItem);
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537 colourMenu.add(clustalColour);
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538 colourMenu.add(BLOSUM62Colour);
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539 colourMenu.add(PIDColour);
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540 colourMenu.add(zappoColour);
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541 colourMenu.add(taylorColour);
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542 colourMenu.add(hydrophobicityColour);
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543 colourMenu.add(helixColour);
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544 colourMenu.add(strandColour);
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545 colourMenu.add(turnColour);
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546 colourMenu.add(buriedColour);
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547 colourMenu.add(nucleotideMenuItem);
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548 colourMenu.add(userDefinedColour);
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550 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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552 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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553 getUserColourSchemes().keys();
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555 while (userColours.hasMoreElements())
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557 JMenuItem item = new JMenuItem(userColours.
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558 nextElement().toString());
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559 item.addActionListener(new ActionListener()
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561 public void actionPerformed(ActionEvent evt)
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563 userDefinedColour_actionPerformed(evt);
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566 colourMenu.add(item);
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571 colourMenu.addSeparator();
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572 colourMenu.add(abovePIDColour);
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573 colourMenu.add(conservationMenuItem);
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574 editMenu.add(copy);
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576 editMenu.add(upperCase);
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577 editMenu.add(lowerCase);
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578 editMenu.add(toggle);
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579 pdbMenu.add(pdbFromFile);
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580 pdbMenu.add(enterPDB);
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581 pdbMenu.add(discoverPDB);
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582 jMenu1.add(groupName);
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583 jMenu1.add(unGroupMenuItem);
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584 jMenu1.add(colourMenu);
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585 jMenu1.add(showBoxes);
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586 jMenu1.add(showText);
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587 jMenu1.add(showColourText);
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588 jMenu1.add(outline);
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589 noColourmenuItem.setText("None");
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590 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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592 public void actionPerformed(ActionEvent e)
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594 noColourmenuItem_actionPerformed(e);
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598 clustalColour.setText("Clustalx colours");
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599 clustalColour.addActionListener(new java.awt.event.ActionListener()
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601 public void actionPerformed(ActionEvent e)
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603 clustalColour_actionPerformed(e);
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606 zappoColour.setText("Zappo");
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607 zappoColour.addActionListener(new java.awt.event.ActionListener()
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609 public void actionPerformed(ActionEvent e)
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611 zappoColour_actionPerformed(e);
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614 taylorColour.setText("Taylor");
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615 taylorColour.addActionListener(new java.awt.event.ActionListener()
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617 public void actionPerformed(ActionEvent e)
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619 taylorColour_actionPerformed(e);
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622 hydrophobicityColour.setText("Hydrophobicity");
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623 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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625 public void actionPerformed(ActionEvent e)
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627 hydrophobicityColour_actionPerformed(e);
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630 helixColour.setText("Helix propensity");
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631 helixColour.addActionListener(new java.awt.event.ActionListener()
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633 public void actionPerformed(ActionEvent e)
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635 helixColour_actionPerformed(e);
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638 strandColour.setText("Strand propensity");
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639 strandColour.addActionListener(new java.awt.event.ActionListener()
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641 public void actionPerformed(ActionEvent e)
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643 strandColour_actionPerformed(e);
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646 turnColour.setText("Turn propensity");
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647 turnColour.addActionListener(new java.awt.event.ActionListener()
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649 public void actionPerformed(ActionEvent e)
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651 turnColour_actionPerformed(e);
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654 buriedColour.setText("Buried Index");
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655 buriedColour.addActionListener(new java.awt.event.ActionListener()
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657 public void actionPerformed(ActionEvent e)
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659 buriedColour_actionPerformed(e);
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662 abovePIDColour.setText("Above % Identity");
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663 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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665 public void actionPerformed(ActionEvent e)
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667 abovePIDColour_actionPerformed(e);
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670 userDefinedColour.setText("User Defined...");
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671 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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673 public void actionPerformed(ActionEvent e)
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675 userDefinedColour_actionPerformed(e);
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678 PIDColour.setText("Percentage Identity");
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679 PIDColour.addActionListener(new java.awt.event.ActionListener()
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681 public void actionPerformed(ActionEvent e)
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683 PIDColour_actionPerformed(e);
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686 BLOSUM62Colour.setText("BLOSUM62");
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687 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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689 public void actionPerformed(ActionEvent e)
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691 BLOSUM62Colour_actionPerformed(e);
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694 conservationMenuItem.setText("Conservation");
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695 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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697 public void actionPerformed(ActionEvent e)
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699 conservationMenuItem_actionPerformed(e);
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709 if (ap.overviewPanel != null)
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710 ap.overviewPanel.updateOverviewImage();
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712 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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718 * @param e DOCUMENT ME!
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720 protected void clustalColour_actionPerformed(ActionEvent e)
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722 SequenceGroup sg = getGroup();
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723 sg.cs = new ClustalxColourScheme(sg.getSequences(true),
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724 ap.av.alignment.getWidth());
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731 * @param e DOCUMENT ME!
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733 protected void zappoColour_actionPerformed(ActionEvent e)
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735 getGroup().cs = new ZappoColourScheme();
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742 * @param e DOCUMENT ME!
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744 protected void taylorColour_actionPerformed(ActionEvent e)
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746 getGroup().cs = new TaylorColourScheme();
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753 * @param e DOCUMENT ME!
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755 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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757 getGroup().cs = new HydrophobicColourScheme();
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764 * @param e DOCUMENT ME!
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766 protected void helixColour_actionPerformed(ActionEvent e)
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768 getGroup().cs = new HelixColourScheme();
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775 * @param e DOCUMENT ME!
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777 protected void strandColour_actionPerformed(ActionEvent e)
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779 getGroup().cs = new StrandColourScheme();
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786 * @param e DOCUMENT ME!
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788 protected void turnColour_actionPerformed(ActionEvent e)
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790 getGroup().cs = new TurnColourScheme();
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797 * @param e DOCUMENT ME!
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799 protected void buriedColour_actionPerformed(ActionEvent e)
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801 getGroup().cs = new BuriedColourScheme();
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808 * @param e DOCUMENT ME!
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810 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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812 getGroup().cs = new NucleotideColourScheme();
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819 * @param e DOCUMENT ME!
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821 protected void abovePIDColour_actionPerformed(ActionEvent e)
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823 SequenceGroup sg = getGroup();
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827 if (abovePIDColour.isSelected())
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829 sg.cs.setConsensus(AAFrequency.calculate(
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830 sg.getSequences(true), sg.getStartRes(),
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831 sg.getEndRes() + 1));
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833 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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834 getGroup().getName());
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836 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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838 SliderPanel.showPIDSlider();
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840 else // remove PIDColouring
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842 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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851 * @param e DOCUMENT ME!
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853 protected void userDefinedColour_actionPerformed(ActionEvent e)
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855 SequenceGroup sg = getGroup();
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857 if (e.getActionCommand().equals("User Defined..."))
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858 new UserDefinedColours(ap, sg);
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861 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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862 getUserColourSchemes().get(e.getActionCommand());
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871 * @param e DOCUMENT ME!
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873 protected void PIDColour_actionPerformed(ActionEvent e)
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875 SequenceGroup sg = getGroup();
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876 sg.cs = new PIDColourScheme();
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877 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
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879 sg.getEndRes() + 1));
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886 * @param e DOCUMENT ME!
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888 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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890 SequenceGroup sg = getGroup();
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892 sg.cs = new Blosum62ColourScheme();
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894 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),
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896 sg.getEndRes() + 1));
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904 * @param e DOCUMENT ME!
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906 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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908 getGroup().cs = null;
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915 * @param e DOCUMENT ME!
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917 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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919 SequenceGroup sg = getGroup();
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923 if (conservationMenuItem.isSelected())
\r
925 Conservation c = new Conservation("Group",
\r
926 ResidueProperties.propHash, 3,
\r
927 sg.getSequences(true),
\r
929 sg.getEndRes() + 1);
\r
932 c.verdict(false, ap.av.ConsPercGaps);
\r
934 sg.cs.setConservation(c);
\r
936 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
937 SliderPanel.showConservationSlider();
\r
939 else // remove ConservationColouring
\r
941 sg.cs.setConservation(null);
\r
950 * @param e DOCUMENT ME!
\r
952 protected void groupName_actionPerformed(ActionEvent e)
\r
954 SequenceGroup sg = getGroup();
\r
955 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
956 "Enter new group name", "Edit group name",
\r
957 JOptionPane.QUESTION_MESSAGE);
\r
965 groupName.setText(reply);
\r
972 * @return DOCUMENT ME!
\r
974 SequenceGroup getGroup()
\r
976 SequenceGroup sg = ap.av.getSelectionGroup();
\r
977 // this method won't add a new group if it already exists
\r
979 ap.av.alignment.addGroup(sg);
\r
987 * @param e DOCUMENT ME!
\r
989 void sequenceName_actionPerformed(ActionEvent e)
\r
991 JLabel idlabel = new JLabel( " Sequence Name ");
\r
992 JLabel desclabel = new JLabel("Sequence Description ");
\r
993 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
994 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
995 JTextField id = new JTextField(sequence.getName(), 40);
\r
996 JTextField description = new JTextField(sequence.getDescription(), 40);
\r
997 JPanel panel = new JPanel(new BorderLayout());
\r
998 JPanel panel2 = new JPanel(new BorderLayout());
\r
999 panel2.add(idlabel, BorderLayout.WEST);
\r
1000 panel2.add(id, BorderLayout.CENTER);
\r
1001 panel.add(panel2, BorderLayout.NORTH);
\r
1002 panel2 = new JPanel(new BorderLayout());
\r
1003 panel2.add(desclabel, BorderLayout.WEST);
\r
1004 panel2.add(description, BorderLayout.CENTER);
\r
1005 panel.add(panel2, BorderLayout.SOUTH);
\r
1008 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
1009 panel, "Edit Sequence Name/Description",
\r
1010 JOptionPane.OK_CANCEL_OPTION );
\r
1013 if (reply != JOptionPane.OK_OPTION )
\r
1018 String s = id.getText();
\r
1022 if (s.indexOf(" ") > -1)
\r
1024 JOptionPane.showMessageDialog(ap,
\r
1025 "Spaces have been converted to \"_\"",
\r
1026 "No spaces allowed in Sequence Name",
\r
1027 JOptionPane.WARNING_MESSAGE);
\r
1030 s = s.replace(' ', '_');
\r
1031 sequence.setName(s);
\r
1035 sequence.setDescription(description.getText());
\r
1037 ap.av.firePropertyChange("alignment", null,
\r
1038 ap.av.getAlignment().getSequences());
\r
1045 * @param e DOCUMENT ME!
\r
1047 void unGroupMenuItem_actionPerformed(ActionEvent e)
\r
1049 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1050 ap.av.alignment.deleteGroup(sg);
\r
1051 ap.av.setSelectionGroup(null);
\r
1059 * @param e DOCUMENT ME!
\r
1061 protected void outline_actionPerformed(ActionEvent e)
\r
1063 SequenceGroup sg = getGroup();
\r
1064 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1069 sg.setOutlineColour(col);
\r
1078 * @param e DOCUMENT ME!
\r
1080 public void showBoxes_actionPerformed(ActionEvent e)
\r
1082 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1089 * @param e DOCUMENT ME!
\r
1091 public void showText_actionPerformed(ActionEvent e)
\r
1093 getGroup().setDisplayText(showText.isSelected());
\r
1100 * @param e DOCUMENT ME!
\r
1102 public void showColourText_actionPerformed(ActionEvent e)
\r
1104 getGroup().setColourText(showColourText.isSelected());
\r
1108 public void showLink(String url)
\r
1112 jalview.util.BrowserLauncher.openURL(url);
\r
1114 catch (Exception ex)
\r
1116 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1117 "Unixers: Couldn't find default web browser."
\r
1118 +"\nAdd the full path to your browser in Preferences.",
\r
1119 "Web browser not found", JOptionPane.WARNING_MESSAGE );
\r
1122 ex.printStackTrace();
\r
1126 void hideSequences(boolean representGroup)
\r
1128 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1129 if(sg==null || sg.getSize(false)<1)
\r
1131 ap.av.hideSequence(new SequenceI[]{sequence});
\r
1135 int gsize = sg.getSize(false);
\r
1136 SequenceI [] hseqs;
\r
1138 hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
\r
1141 for(int i=0; i<gsize; i++)
\r
1143 if(representGroup && sg.getSequenceAt(i)!=sequence)
\r
1145 sequence.addHiddenSequence(sg.getSequenceAt(i));
\r
1146 hseqs[index++] = sg.getSequenceAt(i);
\r
1148 else if(!representGroup)
\r
1150 hseqs[index++] = sg.getSequenceAt(i);
\r
1154 ap.av.hideSequence(hseqs);
\r
1156 ap.av.setSelectionGroup(null);
\r
1159 public void copy_actionPerformed(ActionEvent e)
\r
1161 ap.alignFrame.copy_actionPerformed(null);
\r
1164 public void cut_actionPerformed(ActionEvent e)
\r
1166 ap.alignFrame.cut_actionPerformed(null);
\r
1169 void changeCase(ActionEvent e)
\r
1171 Object source = e.getSource();
\r
1172 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1173 Vector regions = new Vector();
\r
1176 int start = sg.getStartRes();
\r
1177 int end = sg.getEndRes() + 1;
\r
1181 if (ap.av.hasHiddenColumns)
\r
1184 start = ap.av.colSel.adjustForHiddenColumns(start);
\r
1186 end = ap.av.colSel.getHiddenBoundaryRight(start);
\r
1188 end = sg.getEndRes() + 1;
\r
1189 if (end > sg.getEndRes())
\r
1190 end = sg.getEndRes() + 1;
\r
1193 regions.addElement(new int[]
\r
1196 if (ap.av.hasHiddenColumns)
\r
1198 start = ap.av.colSel.adjustForHiddenColumns(end);
\r
1199 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
\r
1202 while (end < sg.getEndRes());
\r
1204 int[][] startEnd = new int[regions.size()][2];
\r
1205 for (int i = 0; i < regions.size(); i++)
\r
1207 startEnd[i] = (int[]) regions.elementAt(i);
\r
1211 String description;
\r
1214 if(source==toggle)
\r
1216 description = "Toggle Case";
\r
1217 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1219 else if(source==upperCase)
\r
1221 description = "To Upper Case";
\r
1222 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1226 description = "To Lower Case";
\r
1227 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1230 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1231 description, sg.getSequencesAsArray(true), startEnd, caseChange
\r
1234 ap.alignFrame.addHistoryItem(caseCommand);
\r
1237 ap.av.firePropertyChange("alignment", null,
\r
1238 ap.av.getAlignment().getSequences());
\r
1243 public void outputText_actionPerformed(ActionEvent e)
\r
1245 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1246 cap.setForInput(null);
\r
1247 Desktop.addInternalFrame(cap,
\r
1248 "Alignment output - " + e.getActionCommand(), 600,
\r
1251 String [] omitHidden = null;
\r
1253 if(ap.av.hasHiddenColumns)
\r
1255 System.out.println("PROMPT USER HERE");
\r
1256 omitHidden = ap.av.getViewAsString(true);
\r
1259 cap.setText(new FormatAdapter().formatSequences(
\r
1260 e.getActionCommand(),
\r
1261 ap.av.getSelectionAsNewSequence(),
\r
1266 public void pdbFromFile_actionPerformed(ActionEvent e)
\r
1268 jalview.io.JalviewFileChooser chooser
\r
1269 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1271 "LAST_DIRECTORY"));
\r
1272 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1273 chooser.setDialogTitle("Select a PDB file");
\r
1274 chooser.setToolTipText("Load a PDB file");
\r
1276 int value = chooser.showOpenDialog(null);
\r
1278 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1280 PDBEntry entry = new PDBEntry();
\r
1281 String choice = chooser.getSelectedFile().getPath();
\r
1282 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1285 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1286 jalview.io.AppletFormatAdapter.FILE);
\r
1288 if (pdbfile.id == null)
\r
1290 String reply = JOptionPane.showInternalInputDialog(
\r
1292 "Couldn't find a PDB id in the file supplied."
\r
1293 + "Please enter an Id to identify this structure.",
\r
1294 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1295 if (reply == null)
\r
1298 entry.setId(reply);
\r
1301 entry.setId(pdbfile.id);
\r
1303 catch (java.io.IOException ex)
\r
1305 ex.printStackTrace();
\r
1308 entry.setFile(choice);
\r
1309 sequence.getDatasetSequence().addPDBId(entry);
\r
1314 public void enterPDB_actionPerformed(ActionEvent e)
\r
1316 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1317 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1319 if (id != null && id.length() > 0)
\r
1321 PDBEntry entry = new PDBEntry();
\r
1323 sequence.getDatasetSequence()
\r
1328 public void discoverPDB_actionPerformed(ActionEvent e)
\r
1330 new jalview.io.DBRefFetcher(
\r
1331 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r
1334 public void sequenceFeature_actionPerformed(ActionEvent e)
\r
1336 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1340 int gSize= sg.getSize(false);
\r
1341 SequenceI [] seqs = new SequenceI[gSize];
\r
1342 SequenceFeature [] features = new SequenceFeature[gSize];
\r
1344 for (int i = 0; i < gSize; i++)
\r
1346 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1347 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1348 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1349 features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
\r
1352 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1353 .createNewFeatures(seqs, features))
\r
1355 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1356 ap.av.setShowSequenceFeatures(true);
\r
1357 ap.highlightSearchResults(null);
\r
1361 public void textColour_actionPerformed(ActionEvent e)
\r
1363 final SequenceGroup sg = getGroup();
\r
1365 int original1 = sg.textColour.getRGB();
\r
1366 int original2 = sg.textColour2.getRGB();
\r
1367 int thresh = sg.thresholdTextColour;
\r
1368 final JSlider slider = new JSlider(0, 750,sg.thresholdTextColour);
\r
1369 final JButton col1 = new JButton("DARK");
\r
1370 col1.setBackground(sg.textColour);
\r
1371 col1.setForeground(sg.textColour);
\r
1372 final JButton col2 = new JButton("LIGHT");
\r
1373 col2.setBackground(sg.textColour2);
\r
1374 col2.setForeground(sg.textColour2);
\r
1375 final JPanel bigpanel = new JPanel(new BorderLayout());
\r
1376 JPanel panel = new JPanel();
\r
1377 bigpanel.add(panel, BorderLayout.CENTER);
\r
1378 bigpanel.add(new JLabel(
\r
1379 "<html><i>Select a dark and light text colour, then set the threshold to"
\r
1380 +"<br>switch between colours, based on background colour</i></html>"),
\r
1381 BorderLayout.NORTH);
\r
1383 panel.add(slider);
\r
1386 col1.addActionListener(new ActionListener()
\r
1388 public void actionPerformed(ActionEvent e)
\r
1390 Color col = JColorChooser.showDialog(bigpanel,
\r
1391 "Select Colour for Text",
\r
1395 sg.textColour = col;
\r
1396 col1.setBackground(col);
\r
1397 col1.setForeground(col);
\r
1403 col2.addActionListener(new ActionListener()
\r
1405 public void actionPerformed(ActionEvent e)
\r
1407 Color col = JColorChooser.showDialog(bigpanel,
\r
1408 "Select Colour for Text",
\r
1412 sg.textColour2 = col;
\r
1413 col2.setBackground(col);
\r
1414 col2.setForeground(col);
\r
1421 slider.addChangeListener(new ChangeListener()
\r
1423 public void stateChanged(ChangeEvent evt)
\r
1425 sg.thresholdTextColour = slider.getValue();
\r
1430 int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
\r
1432 "Adjust Foreground Text Colour Threshold",
\r
1433 JOptionPane.OK_CANCEL_OPTION,
\r
1434 JOptionPane.QUESTION_MESSAGE,
\r
1438 if(reply==JOptionPane.CANCEL_OPTION)
\r
1440 sg.textColour = new Color(original1);
\r
1441 sg.textColour2 = new Color(original2);
\r
1442 sg.thresholdTextColour = thresh;
\r