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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164 Vector seqs = new Vector();
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165 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
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167 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
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171 for(int p=0; p<pdbs.size(); p++)
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173 PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
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174 if(p1.getId().equals(pdb.getId()))
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176 if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
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177 seqs.addElement(ap.av.alignment.getSequenceAt(i));
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185 SequenceI [] seqs2 = new SequenceI[seqs.size()];
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186 seqs.toArray(seqs2);
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188 new AppJMol(pdb, seqs2, ap);
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191 sequenceMenu.add(menuItem);
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195 menuItem = new JMenuItem("Hide Sequences");
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196 menuItem.addActionListener(new java.awt.event.ActionListener()
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198 public void actionPerformed(ActionEvent e)
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200 hideSequences(false);
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205 if (ap.av.getSelectionGroup() != null
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206 && ap.av.getSelectionGroup().getSize() > 1)
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208 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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209 menuItem.addActionListener(new java.awt.event.ActionListener()
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211 public void actionPerformed(ActionEvent e)
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213 hideSequences(true);
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216 sequenceMenu.add(menuItem);
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219 if (ap.av.hasHiddenRows)
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221 final int index = ap.av.alignment.findIndex(seq);
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223 if (ap.av.adjustForHiddenSeqs(index) -
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224 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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226 menuItem = new JMenuItem("Reveal Sequences");
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227 menuItem.addActionListener(new ActionListener()
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229 public void actionPerformed(ActionEvent e)
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231 ap.av.showSequence(index);
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232 if (ap.overviewPanel != null)
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234 ap.overviewPanel.updateOverviewImage();
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241 menuItem = new JMenuItem("Reveal All");
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242 menuItem.addActionListener(new ActionListener()
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244 public void actionPerformed(ActionEvent e)
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246 ap.av.showAllHiddenSeqs();
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247 if (ap.overviewPanel != null)
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249 ap.overviewPanel.updateOverviewImage();
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259 SequenceGroup sg = ap.av.getSelectionGroup();
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263 groupName.setText(sg.getName());
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265 if (sg.cs instanceof ZappoColourScheme)
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267 zappoColour.setSelected(true);
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269 else if (sg.cs instanceof TaylorColourScheme)
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271 taylorColour.setSelected(true);
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273 else if (sg.cs instanceof PIDColourScheme)
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275 PIDColour.setSelected(true);
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277 else if (sg.cs instanceof Blosum62ColourScheme)
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279 BLOSUM62Colour.setSelected(true);
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281 else if (sg.cs instanceof UserColourScheme)
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283 userDefinedColour.setSelected(true);
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285 else if (sg.cs instanceof HydrophobicColourScheme)
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287 hydrophobicityColour.setSelected(true);
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289 else if (sg.cs instanceof HelixColourScheme)
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291 helixColour.setSelected(true);
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293 else if (sg.cs instanceof StrandColourScheme)
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295 strandColour.setSelected(true);
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297 else if (sg.cs instanceof TurnColourScheme)
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299 turnColour.setSelected(true);
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301 else if (sg.cs instanceof BuriedColourScheme)
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303 buriedColour.setSelected(true);
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305 else if (sg.cs instanceof ClustalxColourScheme)
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307 clustalColour.setSelected(true);
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311 noColourmenuItem.setSelected(true);
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314 if (sg.cs != null && sg.cs.conservationApplied())
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316 conservationMenuItem.setSelected(true);
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319 showText.setSelected(sg.getDisplayText());
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320 showColourText.setSelected(sg.getColourText());
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321 showBoxes.setSelected(sg.getDisplayBoxes());
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325 groupMenu.setVisible(false);
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326 editMenu.setVisible(false);
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329 if (!ap.av.alignment.getGroups().contains(sg))
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331 unGroupMenuItem.setVisible(false);
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336 sequenceMenu.setVisible(false);
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337 pdbMenu.setVisible(false);
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340 if (links != null && links.size() > 0)
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342 JMenu linkMenu = new JMenu("Link");
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344 for (int i = 0; i < links.size(); i++)
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346 String link = links.elementAt(i).toString();
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347 final String label = link.substring(0, link.indexOf("|"));
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348 item = new JMenuItem(label);
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351 if (link.indexOf("$SEQUENCE_ID$") > -1)
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353 String id = seq.getName();
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354 if (id.indexOf("|") > -1)
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356 id = id.substring(id.lastIndexOf("|") + 1);
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359 url = link.substring(link.indexOf("|") + 1,
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360 link.indexOf("$SEQUENCE_ID$"))
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362 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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366 url = link.substring(link.lastIndexOf("|") + 1);
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369 item.addActionListener(new java.awt.event.ActionListener()
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371 public void actionPerformed(ActionEvent e)
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377 linkMenu.add(item);
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379 if (sequence != null)
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381 sequenceMenu.add(linkMenu);
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393 * @throws Exception DOCUMENT ME!
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395 private void jbInit()
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398 groupMenu.setText("Group");
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399 groupMenu.setText("Selection");
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400 groupName.setText("Name");
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401 groupName.addActionListener(new java.awt.event.ActionListener()
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403 public void actionPerformed(ActionEvent e)
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405 groupName_actionPerformed();
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408 sequenceMenu.setText("Sequence");
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409 sequenceName.setText("Edit Name/Description");
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410 sequenceName.addActionListener(new java.awt.event.ActionListener()
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412 public void actionPerformed(ActionEvent e)
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414 sequenceName_actionPerformed();
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417 PIDColour.setFocusPainted(false);
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418 unGroupMenuItem.setText("Remove Group");
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419 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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421 public void actionPerformed(ActionEvent e)
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423 unGroupMenuItem_actionPerformed();
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427 outline.setText("Border colour");
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428 outline.addActionListener(new java.awt.event.ActionListener()
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430 public void actionPerformed(ActionEvent e)
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432 outline_actionPerformed();
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435 nucleotideMenuItem.setText("Nucleotide");
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436 nucleotideMenuItem.addActionListener(new ActionListener()
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438 public void actionPerformed(ActionEvent e)
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440 nucleotideMenuItem_actionPerformed();
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443 colourMenu.setText("Group Colour");
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444 showBoxes.setText("Boxes");
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445 showBoxes.setState(true);
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446 showBoxes.addActionListener(new ActionListener()
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448 public void actionPerformed(ActionEvent e)
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450 showBoxes_actionPerformed();
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453 showText.setText("Text");
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454 showText.setState(true);
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455 showText.addActionListener(new ActionListener()
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457 public void actionPerformed(ActionEvent e)
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459 showText_actionPerformed();
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462 showColourText.setText("Colour Text");
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463 showColourText.addActionListener(new ActionListener()
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465 public void actionPerformed(ActionEvent e)
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467 showColourText_actionPerformed();
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470 editMenu.setText("Edit");
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471 cut.setText("Cut");
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472 cut.addActionListener(new ActionListener()
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474 public void actionPerformed(ActionEvent e)
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476 cut_actionPerformed();
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479 upperCase.setText("To Upper Case");
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480 upperCase.addActionListener(new ActionListener()
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482 public void actionPerformed(ActionEvent e)
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487 copy.setText("Copy");
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488 copy.addActionListener(new ActionListener()
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490 public void actionPerformed(ActionEvent e)
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492 copy_actionPerformed();
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495 lowerCase.setText("To Lower Case");
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496 lowerCase.addActionListener(new ActionListener()
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498 public void actionPerformed(ActionEvent e)
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503 toggle.setText("Toggle Case");
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504 toggle.addActionListener(new ActionListener()
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506 public void actionPerformed(ActionEvent e)
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511 pdbMenu.setText("Associate Structure with Sequence");
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512 pdbFromFile.setText("From File");
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513 pdbFromFile.addActionListener(new ActionListener()
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515 public void actionPerformed(ActionEvent e)
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517 pdbFromFile_actionPerformed();
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520 enterPDB.setText("Enter PDB Id");
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521 enterPDB.addActionListener(new ActionListener()
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523 public void actionPerformed(ActionEvent e)
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525 enterPDB_actionPerformed();
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528 discoverPDB.setText("Discover PDB ids");
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529 discoverPDB.addActionListener(new ActionListener()
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531 public void actionPerformed(ActionEvent e)
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533 discoverPDB_actionPerformed();
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536 outputMenu.setText("Output to Textbox...");
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537 sequenceFeature.setText("Create Sequence Feature");
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538 sequenceFeature.addActionListener(new ActionListener()
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540 public void actionPerformed(ActionEvent e)
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542 sequenceFeature_actionPerformed();
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545 textColour.setText("Text Colour");
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546 textColour.addActionListener(new ActionListener()
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548 public void actionPerformed(ActionEvent e)
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550 textColour_actionPerformed();
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553 jMenu1.setText("Group");
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557 groupMenu.add(editMenu);
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558 groupMenu.add(outputMenu);
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559 groupMenu.add(sequenceFeature);
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560 groupMenu.add(jMenu1);
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561 sequenceMenu.add(sequenceName);
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562 sequenceMenu.add(pdbMenu);
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563 colourMenu.add(textColour);
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564 colourMenu.add(noColourmenuItem);
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565 colourMenu.add(clustalColour);
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566 colourMenu.add(BLOSUM62Colour);
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567 colourMenu.add(PIDColour);
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568 colourMenu.add(zappoColour);
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569 colourMenu.add(taylorColour);
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570 colourMenu.add(hydrophobicityColour);
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571 colourMenu.add(helixColour);
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572 colourMenu.add(strandColour);
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573 colourMenu.add(turnColour);
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574 colourMenu.add(buriedColour);
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575 colourMenu.add(nucleotideMenuItem);
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576 colourMenu.add(userDefinedColour);
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578 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
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580 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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581 getUserColourSchemes().keys();
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583 while (userColours.hasMoreElements())
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585 JMenuItem item = new JMenuItem(userColours.
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586 nextElement().toString());
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587 item.addActionListener(new ActionListener()
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589 public void actionPerformed(ActionEvent evt)
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591 userDefinedColour_actionPerformed(evt);
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594 colourMenu.add(item);
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598 colourMenu.addSeparator();
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599 colourMenu.add(abovePIDColour);
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600 colourMenu.add(conservationMenuItem);
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601 editMenu.add(copy);
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603 editMenu.add(upperCase);
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604 editMenu.add(lowerCase);
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605 editMenu.add(toggle);
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606 pdbMenu.add(pdbFromFile);
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607 pdbMenu.add(enterPDB);
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608 pdbMenu.add(discoverPDB);
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609 jMenu1.add(groupName);
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610 jMenu1.add(unGroupMenuItem);
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611 jMenu1.add(colourMenu);
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612 jMenu1.add(showBoxes);
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613 jMenu1.add(showText);
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614 jMenu1.add(showColourText);
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615 jMenu1.add(outline);
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616 noColourmenuItem.setText("None");
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617 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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619 public void actionPerformed(ActionEvent e)
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621 noColourmenuItem_actionPerformed();
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625 clustalColour.setText("Clustalx colours");
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626 clustalColour.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 clustalColour_actionPerformed();
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633 zappoColour.setText("Zappo");
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634 zappoColour.addActionListener(new java.awt.event.ActionListener()
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636 public void actionPerformed(ActionEvent e)
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638 zappoColour_actionPerformed();
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641 taylorColour.setText("Taylor");
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642 taylorColour.addActionListener(new java.awt.event.ActionListener()
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644 public void actionPerformed(ActionEvent e)
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646 taylorColour_actionPerformed();
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649 hydrophobicityColour.setText("Hydrophobicity");
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650 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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652 public void actionPerformed(ActionEvent e)
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654 hydrophobicityColour_actionPerformed();
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657 helixColour.setText("Helix propensity");
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658 helixColour.addActionListener(new java.awt.event.ActionListener()
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660 public void actionPerformed(ActionEvent e)
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662 helixColour_actionPerformed();
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665 strandColour.setText("Strand propensity");
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666 strandColour.addActionListener(new java.awt.event.ActionListener()
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668 public void actionPerformed(ActionEvent e)
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670 strandColour_actionPerformed();
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673 turnColour.setText("Turn propensity");
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674 turnColour.addActionListener(new java.awt.event.ActionListener()
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676 public void actionPerformed(ActionEvent e)
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678 turnColour_actionPerformed();
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681 buriedColour.setText("Buried Index");
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682 buriedColour.addActionListener(new java.awt.event.ActionListener()
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684 public void actionPerformed(ActionEvent e)
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686 buriedColour_actionPerformed();
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689 abovePIDColour.setText("Above % Identity");
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690 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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692 public void actionPerformed(ActionEvent e)
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694 abovePIDColour_actionPerformed();
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697 userDefinedColour.setText("User Defined...");
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698 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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700 public void actionPerformed(ActionEvent e)
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702 userDefinedColour_actionPerformed(e);
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705 PIDColour.setText("Percentage Identity");
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706 PIDColour.addActionListener(new java.awt.event.ActionListener()
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708 public void actionPerformed(ActionEvent e)
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710 PIDColour_actionPerformed();
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713 BLOSUM62Colour.setText("BLOSUM62");
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714 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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716 public void actionPerformed(ActionEvent e)
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718 BLOSUM62Colour_actionPerformed();
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721 conservationMenuItem.setText("Conservation");
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722 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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724 public void actionPerformed(ActionEvent e)
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726 conservationMenuItem_actionPerformed();
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736 ap.paintAlignment(true);
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738 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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744 * @param e DOCUMENT ME!
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746 protected void clustalColour_actionPerformed()
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748 SequenceGroup sg = getGroup();
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749 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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750 ap.av.alignment.getWidth());
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757 * @param e DOCUMENT ME!
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759 protected void zappoColour_actionPerformed()
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761 getGroup().cs = new ZappoColourScheme();
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768 * @param e DOCUMENT ME!
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770 protected void taylorColour_actionPerformed()
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772 getGroup().cs = new TaylorColourScheme();
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779 * @param e DOCUMENT ME!
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781 protected void hydrophobicityColour_actionPerformed()
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783 getGroup().cs = new HydrophobicColourScheme();
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790 * @param e DOCUMENT ME!
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792 protected void helixColour_actionPerformed()
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794 getGroup().cs = new HelixColourScheme();
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801 * @param e DOCUMENT ME!
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803 protected void strandColour_actionPerformed()
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805 getGroup().cs = new StrandColourScheme();
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812 * @param e DOCUMENT ME!
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814 protected void turnColour_actionPerformed()
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816 getGroup().cs = new TurnColourScheme();
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823 * @param e DOCUMENT ME!
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825 protected void buriedColour_actionPerformed()
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827 getGroup().cs = new BuriedColourScheme();
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834 * @param e DOCUMENT ME!
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836 public void nucleotideMenuItem_actionPerformed()
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838 getGroup().cs = new NucleotideColourScheme();
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845 * @param e DOCUMENT ME!
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847 protected void abovePIDColour_actionPerformed()
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849 SequenceGroup sg = getGroup();
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855 if (abovePIDColour.isSelected())
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857 sg.cs.setConsensus(AAFrequency.calculate(
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858 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
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859 sg.getEndRes() + 1));
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861 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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862 getGroup().getName());
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864 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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866 SliderPanel.showPIDSlider();
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868 else // remove PIDColouring
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870 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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879 * @param e DOCUMENT ME!
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881 protected void userDefinedColour_actionPerformed(ActionEvent e)
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883 SequenceGroup sg = getGroup();
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885 if (e.getActionCommand().equals("User Defined..."))
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887 new UserDefinedColours(ap, sg);
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891 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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892 getUserColourSchemes().get(e.getActionCommand());
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902 * @param e DOCUMENT ME!
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904 protected void PIDColour_actionPerformed()
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906 SequenceGroup sg = getGroup();
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907 sg.cs = new PIDColourScheme();
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908 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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909 hiddenRepSequences),
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911 sg.getEndRes() + 1));
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918 * @param e DOCUMENT ME!
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920 protected void BLOSUM62Colour_actionPerformed()
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922 SequenceGroup sg = getGroup();
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924 sg.cs = new Blosum62ColourScheme();
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926 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
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927 hiddenRepSequences),
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929 sg.getEndRes() + 1));
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937 * @param e DOCUMENT ME!
\r
939 protected void noColourmenuItem_actionPerformed()
\r
941 getGroup().cs = null;
\r
948 * @param e DOCUMENT ME!
\r
950 protected void conservationMenuItem_actionPerformed()
\r
952 SequenceGroup sg = getGroup();
\r
958 if (conservationMenuItem.isSelected())
\r
960 Conservation c = new Conservation("Group",
\r
961 ResidueProperties.propHash, 3,
\r
962 sg.getSequences(ap.av.
\r
963 hiddenRepSequences),
\r
965 sg.getEndRes() + 1);
\r
968 c.verdict(false, ap.av.ConsPercGaps);
\r
970 sg.cs.setConservation(c);
\r
972 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
973 SliderPanel.showConservationSlider();
\r
975 else // remove ConservationColouring
\r
977 sg.cs.setConservation(null);
\r
986 * @param e DOCUMENT ME!
\r
988 protected void groupName_actionPerformed()
\r
991 SequenceGroup sg = getGroup();
\r
992 EditNameDialog dialog = new EditNameDialog(sg.getName(),
\r
993 sg.getDescription(),
\r
995 "Group Description ",
\r
996 "Edit Group Name/Description");
\r
998 if (!dialog.accept)
\r
1003 sg.setName(dialog.getName());
\r
1004 sg.setDescription(dialog.getDescription());
\r
1010 * @return DOCUMENT ME!
\r
1012 SequenceGroup getGroup()
\r
1014 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1015 // this method won't add a new group if it already exists
\r
1018 ap.av.alignment.addGroup(sg);
\r
1027 * @param e DOCUMENT ME!
\r
1029 void sequenceName_actionPerformed()
\r
1031 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
\r
1032 sequence.getDescription(),
\r
1033 " Sequence Name ",
\r
1034 "Sequence Description ",
\r
1035 "Edit Sequence Name/Description");
\r
1037 if (!dialog.accept)
\r
1042 if (dialog.getName() != null)
\r
1044 if (dialog.getName().indexOf(" ") > -1)
\r
1046 JOptionPane.showMessageDialog(ap,
\r
1047 "Spaces have been converted to \"_\"",
\r
1048 "No spaces allowed in Sequence Name",
\r
1049 JOptionPane.WARNING_MESSAGE);
\r
1052 sequence.setName(dialog.getName().replace(' ', '_'));
\r
1053 ap.paintAlignment(false);
\r
1056 sequence.setDescription(dialog.getDescription());
\r
1058 ap.av.firePropertyChange("alignment", null,
\r
1059 ap.av.getAlignment().getSequences());
\r
1066 * @param e DOCUMENT ME!
\r
1068 void unGroupMenuItem_actionPerformed()
\r
1070 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1071 ap.av.alignment.deleteGroup(sg);
\r
1072 ap.av.setSelectionGroup(null);
\r
1079 * @param e DOCUMENT ME!
\r
1081 protected void outline_actionPerformed()
\r
1083 SequenceGroup sg = getGroup();
\r
1084 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1089 sg.setOutlineColour(col);
\r
1098 * @param e DOCUMENT ME!
\r
1100 public void showBoxes_actionPerformed()
\r
1102 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1109 * @param e DOCUMENT ME!
\r
1111 public void showText_actionPerformed()
\r
1113 getGroup().setDisplayText(showText.isSelected());
\r
1120 * @param e DOCUMENT ME!
\r
1122 public void showColourText_actionPerformed()
\r
1124 getGroup().setColourText(showColourText.isSelected());
\r
1128 public void showLink(String url)
\r
1132 jalview.util.BrowserLauncher.openURL(url);
\r
1134 catch (Exception ex)
\r
1136 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1137 "Unixers: Couldn't find default web browser."
\r
1139 "\nAdd the full path to your browser in Preferences.",
\r
1140 "Web browser not found",
\r
1141 JOptionPane.WARNING_MESSAGE);
\r
1143 ex.printStackTrace();
\r
1147 void hideSequences(boolean representGroup)
\r
1149 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1150 if (sg == null || sg.getSize() < 1)
\r
1152 ap.av.hideSequence(new SequenceI[]
\r
1157 ap.av.setSelectionGroup(null);
\r
1159 if (representGroup)
\r
1161 ap.av.hideRepSequences(sequence, sg);
\r
1166 int gsize = sg.getSize();
\r
1167 SequenceI[] hseqs;
\r
1169 hseqs = new SequenceI[gsize];
\r
1172 for (int i = 0; i < gsize; i++)
\r
1174 hseqs[index++] = sg.getSequenceAt(i);
\r
1177 ap.av.hideSequence(hseqs);
\r
1180 public void copy_actionPerformed()
\r
1182 ap.alignFrame.copy_actionPerformed(null);
\r
1185 public void cut_actionPerformed()
\r
1187 ap.alignFrame.cut_actionPerformed(null);
\r
1190 void changeCase(ActionEvent e)
\r
1192 Object source = e.getSource();
\r
1193 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1197 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
\r
1198 sg.getStartRes(), sg.getEndRes() + 1);
\r
1200 String description;
\r
1203 if (source == toggle)
\r
1205 description = "Toggle Case";
\r
1206 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1208 else if (source == upperCase)
\r
1210 description = "To Upper Case";
\r
1211 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1215 description = "To Lower Case";
\r
1216 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1219 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1220 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1221 startEnd, caseChange
\r
1224 ap.alignFrame.addHistoryItem(caseCommand);
\r
1226 ap.av.firePropertyChange("alignment", null,
\r
1227 ap.av.getAlignment().getSequences());
\r
1232 public void outputText_actionPerformed(ActionEvent e)
\r
1234 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1235 cap.setForInput(null);
\r
1236 Desktop.addInternalFrame(cap,
\r
1237 "Alignment output - " + e.getActionCommand(), 600,
\r
1240 String[] omitHidden = null;
\r
1242 if (ap.av.hasHiddenColumns)
\r
1244 System.out.println("PROMPT USER HERE");
\r
1245 omitHidden = ap.av.getViewAsString(true);
\r
1248 cap.setText(new FormatAdapter().formatSequences(
\r
1249 e.getActionCommand(),
\r
1250 ap.av.getSelectionAsNewSequence(),
\r
1254 public void pdbFromFile_actionPerformed()
\r
1256 jalview.io.JalviewFileChooser chooser
\r
1257 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1259 "LAST_DIRECTORY"));
\r
1260 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1261 chooser.setDialogTitle("Select a PDB file");
\r
1262 chooser.setToolTipText("Load a PDB file");
\r
1264 int value = chooser.showOpenDialog(null);
\r
1266 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1268 PDBEntry entry = new PDBEntry();
\r
1269 String choice = chooser.getSelectedFile().getPath();
\r
1270 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1273 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1274 jalview.io.AppletFormatAdapter.FILE);
\r
1276 if (pdbfile.id == null)
\r
1278 String reply = JOptionPane.showInternalInputDialog(
\r
1280 "Couldn't find a PDB id in the file supplied."
\r
1281 + "Please enter an Id to identify this structure.",
\r
1282 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1283 if (reply == null)
\r
1288 entry.setId(reply);
\r
1292 entry.setId(pdbfile.id);
\r
1295 catch (java.io.IOException ex)
\r
1297 ex.printStackTrace();
\r
1300 entry.setFile(choice);
\r
1301 sequence.getDatasetSequence().addPDBId(entry);
\r
1306 public void enterPDB_actionPerformed()
\r
1308 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1309 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1311 if (id != null && id.length() > 0)
\r
1313 PDBEntry entry = new PDBEntry();
\r
1315 sequence.getDatasetSequence()
\r
1320 public void discoverPDB_actionPerformed()
\r
1322 new jalview.io.DBRefFetcher(
\r
1323 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r
1326 public void sequenceFeature_actionPerformed()
\r
1328 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1334 int gSize = sg.getSize();
\r
1335 SequenceI[] seqs = new SequenceI[gSize];
\r
1336 SequenceFeature[] features = new SequenceFeature[gSize];
\r
1338 for (int i = 0; i < gSize; i++)
\r
1340 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1341 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1342 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1343 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
\r
1346 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1347 .createNewFeatures(seqs, features))
\r
1349 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1350 ap.av.setShowSequenceFeatures(true);
\r
1351 ap.highlightSearchResults(null);
\r
1355 public void textColour_actionPerformed()
\r
1357 SequenceGroup sg = getGroup();
\r
1360 new TextColourChooser().chooseColour(ap, sg);
\r