2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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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24 import java.awt.event.*;
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25 import javax.swing.*;
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28 import jalview.analysis.*;
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29 import jalview.commands.*;
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30 import jalview.datamodel.*;
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31 import jalview.io.*;
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32 import jalview.schemes.*;
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38 * @version $Revision$
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40 public class PopupMenu
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43 JMenu groupMenu = new JMenu();
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44 JMenuItem groupName = new JMenuItem();
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45 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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46 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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47 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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48 protected JRadioButtonMenuItem hydrophobicityColour = new
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49 JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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54 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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55 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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58 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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59 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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61 JMenu sequenceMenu = new JMenu();
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62 JMenuItem sequenceName = new JMenuItem();
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64 JMenuItem unGroupMenuItem = new JMenuItem();
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65 JMenuItem outline = new JMenuItem();
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66 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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67 JMenu colourMenu = new JMenu();
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68 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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69 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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70 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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71 JMenu editMenu = new JMenu();
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72 JMenuItem cut = new JMenuItem();
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73 JMenuItem copy = new JMenuItem();
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74 JMenuItem upperCase = new JMenuItem();
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75 JMenuItem lowerCase = new JMenuItem();
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76 JMenuItem toggle = new JMenuItem();
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77 JMenu pdbMenu = new JMenu();
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78 JMenuItem pdbFromFile = new JMenuItem();
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79 JMenuItem enterPDB = new JMenuItem();
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80 JMenuItem discoverPDB = new JMenuItem();
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81 JMenu outputMenu = new JMenu();
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82 JMenuItem sequenceFeature = new JMenuItem();
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83 JMenuItem textColour = new JMenuItem();
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84 JMenu jMenu1 = new JMenu();
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87 * Creates a new PopupMenu object.
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89 * @param ap DOCUMENT ME!
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90 * @param seq DOCUMENT ME!
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92 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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94 ///////////////////////////////////////////////////////////
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95 // If this is activated from the sequence panel, the user may want to
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96 // edit or annotate a particular residue. Therefore display the residue menu
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98 // If from the IDPanel, we must display the sequence menu
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99 //////////////////////////////////////////////////////////
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103 ButtonGroup colours = new ButtonGroup();
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104 colours.add(noColourmenuItem);
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105 colours.add(clustalColour);
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106 colours.add(zappoColour);
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107 colours.add(taylorColour);
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108 colours.add(hydrophobicityColour);
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109 colours.add(helixColour);
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110 colours.add(strandColour);
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111 colours.add(turnColour);
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112 colours.add(buriedColour);
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113 colours.add(abovePIDColour);
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114 colours.add(userDefinedColour);
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115 colours.add(PIDColour);
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116 colours.add(BLOSUM62Colour);
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118 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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120 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
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123 item.addActionListener(new java.awt.event.ActionListener()
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125 public void actionPerformed(ActionEvent e)
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127 outputText_actionPerformed(e);
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131 outputMenu.add(item);
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138 catch (Exception e)
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140 e.printStackTrace();
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145 sequenceMenu.setText(sequence.getName());
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147 JMenuItem menuItem;
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148 if (seq.getDatasetSequence().getPDBId() != null)
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150 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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153 while (e.hasMoreElements())
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155 final PDBEntry pdb = (PDBEntry) e.nextElement();
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157 menuItem = new JMenuItem();
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158 menuItem.setText("View PDB entry: " + pdb.getId());
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159 menuItem.addActionListener(new java.awt.event.ActionListener()
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161 public void actionPerformed(ActionEvent e)
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163 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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166 sequenceMenu.add(menuItem);
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170 menuItem = new JMenuItem("Hide Sequences");
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171 menuItem.addActionListener(new java.awt.event.ActionListener()
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173 public void actionPerformed(ActionEvent e)
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175 hideSequences(false);
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180 if (ap.av.getSelectionGroup() != null
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181 && ap.av.getSelectionGroup().getSize() > 1)
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183 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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184 menuItem.addActionListener(new java.awt.event.ActionListener()
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186 public void actionPerformed(ActionEvent e)
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188 hideSequences(true);
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191 sequenceMenu.add(menuItem);
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194 if (ap.av.hasHiddenRows)
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196 final int index = ap.av.alignment.findIndex(seq);
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198 if (ap.av.adjustForHiddenSeqs(index) -
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199 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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201 menuItem = new JMenuItem("Reveal Sequences");
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202 menuItem.addActionListener(new ActionListener()
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204 public void actionPerformed(ActionEvent e)
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206 ap.av.showSequence(index);
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207 if (ap.overviewPanel != null)
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209 ap.overviewPanel.updateOverviewImage();
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216 menuItem = new JMenuItem("Reveal All");
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217 menuItem.addActionListener(new ActionListener()
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219 public void actionPerformed(ActionEvent e)
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221 ap.av.showAllHiddenSeqs();
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222 if (ap.overviewPanel != null)
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224 ap.overviewPanel.updateOverviewImage();
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234 SequenceGroup sg = ap.av.getSelectionGroup();
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238 groupName.setText(sg.getName());
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240 if (sg.cs instanceof ZappoColourScheme)
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242 zappoColour.setSelected(true);
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244 else if (sg.cs instanceof TaylorColourScheme)
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246 taylorColour.setSelected(true);
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248 else if (sg.cs instanceof PIDColourScheme)
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250 PIDColour.setSelected(true);
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252 else if (sg.cs instanceof Blosum62ColourScheme)
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254 BLOSUM62Colour.setSelected(true);
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256 else if (sg.cs instanceof UserColourScheme)
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258 userDefinedColour.setSelected(true);
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260 else if (sg.cs instanceof HydrophobicColourScheme)
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262 hydrophobicityColour.setSelected(true);
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264 else if (sg.cs instanceof HelixColourScheme)
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266 helixColour.setSelected(true);
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268 else if (sg.cs instanceof StrandColourScheme)
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270 strandColour.setSelected(true);
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272 else if (sg.cs instanceof TurnColourScheme)
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274 turnColour.setSelected(true);
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276 else if (sg.cs instanceof BuriedColourScheme)
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278 buriedColour.setSelected(true);
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280 else if (sg.cs instanceof ClustalxColourScheme)
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282 clustalColour.setSelected(true);
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286 noColourmenuItem.setSelected(true);
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289 if (sg.cs != null && sg.cs.conservationApplied())
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291 conservationMenuItem.setSelected(true);
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294 showText.setSelected(sg.getDisplayText());
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295 showColourText.setSelected(sg.getColourText());
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296 showBoxes.setSelected(sg.getDisplayBoxes());
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300 groupMenu.setVisible(false);
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301 editMenu.setVisible(false);
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304 if (!ap.av.alignment.getGroups().contains(sg))
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306 unGroupMenuItem.setVisible(false);
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311 sequenceMenu.setVisible(false);
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312 pdbMenu.setVisible(false);
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315 if (links != null && links.size() > 0)
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317 JMenu linkMenu = new JMenu("Link");
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319 for (int i = 0; i < links.size(); i++)
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321 String link = links.elementAt(i).toString();
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322 final String label = link.substring(0, link.indexOf("|"));
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323 item = new JMenuItem(label);
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326 if (link.indexOf("$SEQUENCE_ID$") > -1)
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328 String id = seq.getName();
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329 if (id.indexOf("|") > -1)
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331 id = id.substring(id.lastIndexOf("|") + 1);
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334 url = link.substring(link.indexOf("|") + 1,
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335 link.indexOf("$SEQUENCE_ID$"))
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337 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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341 url = link.substring(link.lastIndexOf("|") + 1);
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344 item.addActionListener(new java.awt.event.ActionListener()
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346 public void actionPerformed(ActionEvent e)
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352 linkMenu.add(item);
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354 if (sequence != null)
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356 sequenceMenu.add(linkMenu);
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368 * @throws Exception DOCUMENT ME!
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370 private void jbInit()
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373 groupMenu.setText("Group");
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374 groupMenu.setText("Selection");
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375 groupName.setText("Name");
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376 groupName.addActionListener(new java.awt.event.ActionListener()
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378 public void actionPerformed(ActionEvent e)
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380 groupName_actionPerformed();
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383 sequenceMenu.setText("Sequence");
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384 sequenceName.setText("Edit Name/Description");
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385 sequenceName.addActionListener(new java.awt.event.ActionListener()
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387 public void actionPerformed(ActionEvent e)
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389 sequenceName_actionPerformed();
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392 PIDColour.setFocusPainted(false);
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393 unGroupMenuItem.setText("Remove Group");
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394 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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396 public void actionPerformed(ActionEvent e)
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398 unGroupMenuItem_actionPerformed();
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402 outline.setText("Border colour");
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403 outline.addActionListener(new java.awt.event.ActionListener()
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405 public void actionPerformed(ActionEvent e)
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407 outline_actionPerformed();
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410 nucleotideMenuItem.setText("Nucleotide");
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411 nucleotideMenuItem.addActionListener(new ActionListener()
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413 public void actionPerformed(ActionEvent e)
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415 nucleotideMenuItem_actionPerformed();
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418 colourMenu.setText("Group Colour");
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419 showBoxes.setText("Boxes");
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420 showBoxes.setState(true);
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421 showBoxes.addActionListener(new ActionListener()
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423 public void actionPerformed(ActionEvent e)
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425 showBoxes_actionPerformed();
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428 showText.setText("Text");
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429 showText.setState(true);
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430 showText.addActionListener(new ActionListener()
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432 public void actionPerformed(ActionEvent e)
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434 showText_actionPerformed();
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437 showColourText.setText("Colour Text");
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438 showColourText.addActionListener(new ActionListener()
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440 public void actionPerformed(ActionEvent e)
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442 showColourText_actionPerformed();
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445 editMenu.setText("Edit");
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446 cut.setText("Cut");
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447 cut.addActionListener(new ActionListener()
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449 public void actionPerformed(ActionEvent e)
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451 cut_actionPerformed();
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454 upperCase.setText("To Upper Case");
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455 upperCase.addActionListener(new ActionListener()
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457 public void actionPerformed(ActionEvent e)
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462 copy.setText("Copy");
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463 copy.addActionListener(new ActionListener()
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465 public void actionPerformed(ActionEvent e)
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467 copy_actionPerformed();
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470 lowerCase.setText("To Lower Case");
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471 lowerCase.addActionListener(new ActionListener()
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473 public void actionPerformed(ActionEvent e)
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478 toggle.setText("Toggle Case");
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479 toggle.addActionListener(new ActionListener()
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481 public void actionPerformed(ActionEvent e)
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486 pdbMenu.setText("Associate Structure with Sequence");
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487 pdbFromFile.setText("From File");
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488 pdbFromFile.addActionListener(new ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 pdbFromFile_actionPerformed();
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495 enterPDB.setText("Enter PDB Id");
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496 enterPDB.addActionListener(new ActionListener()
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498 public void actionPerformed(ActionEvent e)
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500 enterPDB_actionPerformed();
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503 discoverPDB.setText("Discover PDB ids");
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504 discoverPDB.addActionListener(new ActionListener()
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506 public void actionPerformed(ActionEvent e)
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508 discoverPDB_actionPerformed();
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511 outputMenu.setText("Output to Textbox...");
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512 sequenceFeature.setText("Create Sequence Feature");
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513 sequenceFeature.addActionListener(new ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 sequenceFeature_actionPerformed();
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520 textColour.setText("Text Colour");
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521 textColour.addActionListener(new ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 textColour_actionPerformed();
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528 jMenu1.setText("Group");
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532 groupMenu.add(editMenu);
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533 groupMenu.add(outputMenu);
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534 groupMenu.add(sequenceFeature);
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535 groupMenu.add(jMenu1);
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536 sequenceMenu.add(sequenceName);
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537 sequenceMenu.add(pdbMenu);
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538 colourMenu.add(textColour);
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539 colourMenu.add(noColourmenuItem);
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540 colourMenu.add(clustalColour);
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541 colourMenu.add(BLOSUM62Colour);
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542 colourMenu.add(PIDColour);
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543 colourMenu.add(zappoColour);
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544 colourMenu.add(taylorColour);
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545 colourMenu.add(hydrophobicityColour);
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546 colourMenu.add(helixColour);
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547 colourMenu.add(strandColour);
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548 colourMenu.add(turnColour);
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549 colourMenu.add(buriedColour);
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550 colourMenu.add(nucleotideMenuItem);
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551 colourMenu.add(userDefinedColour);
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553 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
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555 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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556 getUserColourSchemes().keys();
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558 while (userColours.hasMoreElements())
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560 JMenuItem item = new JMenuItem(userColours.
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561 nextElement().toString());
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562 item.addActionListener(new ActionListener()
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564 public void actionPerformed(ActionEvent evt)
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566 userDefinedColour_actionPerformed(evt);
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569 colourMenu.add(item);
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573 colourMenu.addSeparator();
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574 colourMenu.add(abovePIDColour);
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575 colourMenu.add(conservationMenuItem);
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576 editMenu.add(copy);
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578 editMenu.add(upperCase);
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579 editMenu.add(lowerCase);
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580 editMenu.add(toggle);
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581 pdbMenu.add(pdbFromFile);
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582 pdbMenu.add(enterPDB);
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583 pdbMenu.add(discoverPDB);
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584 jMenu1.add(groupName);
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585 jMenu1.add(unGroupMenuItem);
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586 jMenu1.add(colourMenu);
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587 jMenu1.add(showBoxes);
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588 jMenu1.add(showText);
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589 jMenu1.add(showColourText);
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590 jMenu1.add(outline);
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591 noColourmenuItem.setText("None");
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592 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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594 public void actionPerformed(ActionEvent e)
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596 noColourmenuItem_actionPerformed();
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600 clustalColour.setText("Clustalx colours");
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601 clustalColour.addActionListener(new java.awt.event.ActionListener()
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603 public void actionPerformed(ActionEvent e)
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605 clustalColour_actionPerformed();
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608 zappoColour.setText("Zappo");
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609 zappoColour.addActionListener(new java.awt.event.ActionListener()
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611 public void actionPerformed(ActionEvent e)
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613 zappoColour_actionPerformed();
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616 taylorColour.setText("Taylor");
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617 taylorColour.addActionListener(new java.awt.event.ActionListener()
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619 public void actionPerformed(ActionEvent e)
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621 taylorColour_actionPerformed();
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624 hydrophobicityColour.setText("Hydrophobicity");
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625 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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627 public void actionPerformed(ActionEvent e)
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629 hydrophobicityColour_actionPerformed();
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632 helixColour.setText("Helix propensity");
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633 helixColour.addActionListener(new java.awt.event.ActionListener()
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635 public void actionPerformed(ActionEvent e)
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637 helixColour_actionPerformed();
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640 strandColour.setText("Strand propensity");
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641 strandColour.addActionListener(new java.awt.event.ActionListener()
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643 public void actionPerformed(ActionEvent e)
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645 strandColour_actionPerformed();
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648 turnColour.setText("Turn propensity");
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649 turnColour.addActionListener(new java.awt.event.ActionListener()
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651 public void actionPerformed(ActionEvent e)
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653 turnColour_actionPerformed();
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656 buriedColour.setText("Buried Index");
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657 buriedColour.addActionListener(new java.awt.event.ActionListener()
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659 public void actionPerformed(ActionEvent e)
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661 buriedColour_actionPerformed();
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664 abovePIDColour.setText("Above % Identity");
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665 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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667 public void actionPerformed(ActionEvent e)
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669 abovePIDColour_actionPerformed();
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672 userDefinedColour.setText("User Defined...");
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673 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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675 public void actionPerformed(ActionEvent e)
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677 userDefinedColour_actionPerformed(e);
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680 PIDColour.setText("Percentage Identity");
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681 PIDColour.addActionListener(new java.awt.event.ActionListener()
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683 public void actionPerformed(ActionEvent e)
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685 PIDColour_actionPerformed();
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688 BLOSUM62Colour.setText("BLOSUM62");
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689 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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691 public void actionPerformed(ActionEvent e)
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693 BLOSUM62Colour_actionPerformed();
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696 conservationMenuItem.setText("Conservation");
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697 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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699 public void actionPerformed(ActionEvent e)
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701 conservationMenuItem_actionPerformed();
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711 if (ap.overviewPanel != null)
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713 ap.overviewPanel.updateOverviewImage();
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716 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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722 * @param e DOCUMENT ME!
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724 protected void clustalColour_actionPerformed()
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726 SequenceGroup sg = getGroup();
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727 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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728 ap.av.alignment.getWidth());
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735 * @param e DOCUMENT ME!
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737 protected void zappoColour_actionPerformed()
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739 getGroup().cs = new ZappoColourScheme();
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746 * @param e DOCUMENT ME!
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748 protected void taylorColour_actionPerformed()
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750 getGroup().cs = new TaylorColourScheme();
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757 * @param e DOCUMENT ME!
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759 protected void hydrophobicityColour_actionPerformed()
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761 getGroup().cs = new HydrophobicColourScheme();
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768 * @param e DOCUMENT ME!
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770 protected void helixColour_actionPerformed()
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772 getGroup().cs = new HelixColourScheme();
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779 * @param e DOCUMENT ME!
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781 protected void strandColour_actionPerformed()
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783 getGroup().cs = new StrandColourScheme();
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790 * @param e DOCUMENT ME!
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792 protected void turnColour_actionPerformed()
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794 getGroup().cs = new TurnColourScheme();
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801 * @param e DOCUMENT ME!
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803 protected void buriedColour_actionPerformed()
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805 getGroup().cs = new BuriedColourScheme();
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812 * @param e DOCUMENT ME!
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814 public void nucleotideMenuItem_actionPerformed()
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816 getGroup().cs = new NucleotideColourScheme();
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823 * @param e DOCUMENT ME!
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825 protected void abovePIDColour_actionPerformed()
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827 SequenceGroup sg = getGroup();
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833 if (abovePIDColour.isSelected())
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835 sg.cs.setConsensus(AAFrequency.calculate(
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836 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
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837 sg.getEndRes() + 1));
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839 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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840 getGroup().getName());
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842 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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844 SliderPanel.showPIDSlider();
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846 else // remove PIDColouring
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848 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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857 * @param e DOCUMENT ME!
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859 protected void userDefinedColour_actionPerformed(ActionEvent e)
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861 SequenceGroup sg = getGroup();
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863 if (e.getActionCommand().equals("User Defined..."))
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865 new UserDefinedColours(ap, sg);
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869 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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870 getUserColourSchemes().get(e.getActionCommand());
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880 * @param e DOCUMENT ME!
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882 protected void PIDColour_actionPerformed()
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884 SequenceGroup sg = getGroup();
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885 sg.cs = new PIDColourScheme();
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886 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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887 hiddenRepSequences),
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889 sg.getEndRes() + 1));
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896 * @param e DOCUMENT ME!
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898 protected void BLOSUM62Colour_actionPerformed()
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900 SequenceGroup sg = getGroup();
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902 sg.cs = new Blosum62ColourScheme();
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904 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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905 hiddenRepSequences),
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907 sg.getEndRes() + 1));
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915 * @param e DOCUMENT ME!
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917 protected void noColourmenuItem_actionPerformed()
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919 getGroup().cs = null;
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926 * @param e DOCUMENT ME!
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928 protected void conservationMenuItem_actionPerformed()
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930 SequenceGroup sg = getGroup();
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936 if (conservationMenuItem.isSelected())
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938 Conservation c = new Conservation("Group",
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939 ResidueProperties.propHash, 3,
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940 sg.getSequences(ap.av.
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941 hiddenRepSequences),
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943 sg.getEndRes() + 1);
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946 c.verdict(false, ap.av.ConsPercGaps);
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948 sg.cs.setConservation(c);
\r
950 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
951 SliderPanel.showConservationSlider();
\r
953 else // remove ConservationColouring
\r
955 sg.cs.setConservation(null);
\r
964 * @param e DOCUMENT ME!
\r
966 protected void groupName_actionPerformed()
\r
969 SequenceGroup sg = getGroup();
\r
970 EditNameDialog dialog = new EditNameDialog(sg.getName(),
\r
971 sg.getDescription(),
\r
973 "Group Description ",
\r
974 "Edit Group Name/Description");
\r
976 if (!dialog.accept)
\r
981 sg.setName(dialog.getName());
\r
982 sg.setDescription(dialog.getDescription());
\r
988 * @return DOCUMENT ME!
\r
990 SequenceGroup getGroup()
\r
992 SequenceGroup sg = ap.av.getSelectionGroup();
\r
993 // this method won't add a new group if it already exists
\r
996 ap.av.alignment.addGroup(sg);
\r
1005 * @param e DOCUMENT ME!
\r
1007 void sequenceName_actionPerformed()
\r
1009 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
\r
1010 sequence.getDescription(),
\r
1011 " Sequence Name ",
\r
1012 "Sequence Description ",
\r
1013 "Edit Sequence Name/Description");
\r
1015 if (!dialog.accept)
\r
1020 if (dialog.getName() != null)
\r
1022 if (dialog.getName().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 sequence.setName(dialog.getName().replace(' ', '_'));
\r
1034 sequence.setDescription(dialog.getDescription());
\r
1036 ap.av.firePropertyChange("alignment", null,
\r
1037 ap.av.getAlignment().getSequences());
\r
1044 * @param e DOCUMENT ME!
\r
1046 void unGroupMenuItem_actionPerformed()
\r
1048 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1049 ap.av.alignment.deleteGroup(sg);
\r
1050 ap.av.setSelectionGroup(null);
\r
1057 * @param e DOCUMENT ME!
\r
1059 protected void outline_actionPerformed()
\r
1061 SequenceGroup sg = getGroup();
\r
1062 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1067 sg.setOutlineColour(col);
\r
1076 * @param e DOCUMENT ME!
\r
1078 public void showBoxes_actionPerformed()
\r
1080 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1087 * @param e DOCUMENT ME!
\r
1089 public void showText_actionPerformed()
\r
1091 getGroup().setDisplayText(showText.isSelected());
\r
1098 * @param e DOCUMENT ME!
\r
1100 public void showColourText_actionPerformed()
\r
1102 getGroup().setColourText(showColourText.isSelected());
\r
1106 public void showLink(String url)
\r
1110 jalview.util.BrowserLauncher.openURL(url);
\r
1112 catch (Exception ex)
\r
1114 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1115 "Unixers: Couldn't find default web browser."
\r
1117 "\nAdd the full path to your browser in Preferences.",
\r
1118 "Web browser not found",
\r
1119 JOptionPane.WARNING_MESSAGE);
\r
1121 ex.printStackTrace();
\r
1125 void hideSequences(boolean representGroup)
\r
1127 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1128 if (sg == null || sg.getSize() < 1)
\r
1130 ap.av.hideSequence(new SequenceI[]
\r
1135 ap.av.setSelectionGroup(null);
\r
1137 if (representGroup)
\r
1139 ap.av.hideRepSequences(sequence, sg);
\r
1144 int gsize = sg.getSize();
\r
1145 SequenceI[] hseqs;
\r
1147 hseqs = new SequenceI[gsize];
\r
1150 for (int i = 0; i < gsize; i++)
\r
1152 hseqs[index++] = sg.getSequenceAt(i);
\r
1155 ap.av.hideSequence(hseqs);
\r
1158 public void copy_actionPerformed()
\r
1160 ap.alignFrame.copy_actionPerformed(null);
\r
1163 public void cut_actionPerformed()
\r
1165 ap.alignFrame.cut_actionPerformed(null);
\r
1168 void changeCase(ActionEvent e)
\r
1170 Object source = e.getSource();
\r
1171 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1172 Vector regions = new Vector();
\r
1175 int start = sg.getStartRes();
\r
1176 int end = sg.getEndRes() + 1;
\r
1180 if (ap.av.hasHiddenColumns)
\r
1184 start = ap.av.colSel.adjustForHiddenColumns(start);
\r
1187 end = ap.av.colSel.getHiddenBoundaryRight(start);
\r
1190 end = sg.getEndRes() + 1;
\r
1192 if (end > sg.getEndRes())
\r
1194 end = sg.getEndRes() + 1;
\r
1198 regions.addElement(new int[]
\r
1201 if (ap.av.hasHiddenColumns)
\r
1203 start = ap.av.colSel.adjustForHiddenColumns(end);
\r
1204 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
\r
1207 while (end < sg.getEndRes());
\r
1209 int[][] startEnd = new int[regions.size()][2];
\r
1210 for (int i = 0; i < regions.size(); i++)
\r
1212 startEnd[i] = (int[]) regions.elementAt(i);
\r
1215 String description;
\r
1218 if (source == toggle)
\r
1220 description = "Toggle Case";
\r
1221 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1223 else if (source == upperCase)
\r
1225 description = "To Upper Case";
\r
1226 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1230 description = "To Lower Case";
\r
1231 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1234 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1235 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1236 startEnd, caseChange
\r
1239 ap.alignFrame.addHistoryItem(caseCommand);
\r
1241 ap.av.firePropertyChange("alignment", null,
\r
1242 ap.av.getAlignment().getSequences());
\r
1247 public void outputText_actionPerformed(ActionEvent e)
\r
1249 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1250 cap.setForInput(null);
\r
1251 Desktop.addInternalFrame(cap,
\r
1252 "Alignment output - " + e.getActionCommand(), 600,
\r
1255 String[] omitHidden = null;
\r
1257 if (ap.av.hasHiddenColumns)
\r
1259 System.out.println("PROMPT USER HERE");
\r
1260 omitHidden = ap.av.getViewAsString(true);
\r
1263 cap.setText(new FormatAdapter().formatSequences(
\r
1264 e.getActionCommand(),
\r
1265 ap.av.getSelectionAsNewSequence(),
\r
1269 public void pdbFromFile_actionPerformed()
\r
1271 jalview.io.JalviewFileChooser chooser
\r
1272 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1274 "LAST_DIRECTORY"));
\r
1275 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1276 chooser.setDialogTitle("Select a PDB file");
\r
1277 chooser.setToolTipText("Load a PDB file");
\r
1279 int value = chooser.showOpenDialog(null);
\r
1281 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1283 PDBEntry entry = new PDBEntry();
\r
1284 String choice = chooser.getSelectedFile().getPath();
\r
1285 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1288 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1289 jalview.io.AppletFormatAdapter.FILE);
\r
1291 if (pdbfile.id == null)
\r
1293 String reply = JOptionPane.showInternalInputDialog(
\r
1295 "Couldn't find a PDB id in the file supplied."
\r
1296 + "Please enter an Id to identify this structure.",
\r
1297 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1298 if (reply == null)
\r
1303 entry.setId(reply);
\r
1307 entry.setId(pdbfile.id);
\r
1310 catch (java.io.IOException ex)
\r
1312 ex.printStackTrace();
\r
1315 entry.setFile(choice);
\r
1316 sequence.getDatasetSequence().addPDBId(entry);
\r
1321 public void enterPDB_actionPerformed()
\r
1323 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1324 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1326 if (id != null && id.length() > 0)
\r
1328 PDBEntry entry = new PDBEntry();
\r
1330 sequence.getDatasetSequence()
\r
1335 public void discoverPDB_actionPerformed()
\r
1337 new jalview.io.DBRefFetcher(
\r
1338 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r
1341 public void sequenceFeature_actionPerformed()
\r
1343 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1349 int gSize = sg.getSize();
\r
1350 SequenceI[] seqs = new SequenceI[gSize];
\r
1351 SequenceFeature[] features = new SequenceFeature[gSize];
\r
1353 for (int i = 0; i < gSize; i++)
\r
1355 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1356 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1357 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1358 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
\r
1361 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1362 .createNewFeatures(seqs, features))
\r
1364 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1365 ap.av.setShowSequenceFeatures(true);
\r
1366 ap.highlightSearchResults(null);
\r
1370 public void textColour_actionPerformed()
\r
1372 SequenceGroup sg = getGroup();
\r
1375 new TextColourChooser().chooseColour(ap, sg);
\r