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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85 JMenu structureMenu = new JMenu();
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86 JMenu viewStructureMenu = new JMenu();
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87 JMenu colStructureMenu = new JMenu();
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90 * Creates a new PopupMenu object.
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92 * @param ap DOCUMENT ME!
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93 * @param seq DOCUMENT ME!
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95 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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97 ///////////////////////////////////////////////////////////
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98 // If this is activated from the sequence panel, the user may want to
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99 // edit or annotate a particular residue. Therefore display the residue menu
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101 // If from the IDPanel, we must display the sequence menu
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102 //////////////////////////////////////////////////////////
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106 ButtonGroup colours = new ButtonGroup();
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107 colours.add(noColourmenuItem);
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108 colours.add(clustalColour);
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109 colours.add(zappoColour);
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110 colours.add(taylorColour);
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111 colours.add(hydrophobicityColour);
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112 colours.add(helixColour);
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113 colours.add(strandColour);
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114 colours.add(turnColour);
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115 colours.add(buriedColour);
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116 colours.add(abovePIDColour);
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117 colours.add(userDefinedColour);
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118 colours.add(PIDColour);
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119 colours.add(BLOSUM62Colour);
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121 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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123 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
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126 item.addActionListener(new java.awt.event.ActionListener()
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128 public void actionPerformed(ActionEvent e)
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130 outputText_actionPerformed(e);
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134 outputMenu.add(item);
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141 catch (Exception e)
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143 e.printStackTrace();
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148 sequenceMenu.setText(sequence.getName());
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150 JMenuItem menuItem;
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151 if (seq.getDatasetSequence().getPDBId() != null)
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153 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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156 while (e.hasMoreElements())
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158 final PDBEntry pdb = (PDBEntry) e.nextElement();
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160 menuItem = new JMenuItem();
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161 menuItem.setText(pdb.getId());
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162 menuItem.addActionListener(new java.awt.event.ActionListener()
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164 public void actionPerformed(ActionEvent e)
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166 Vector seqs = new Vector();
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167 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
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169 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
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173 for(int p=0; p<pdbs.size(); p++)
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175 PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
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176 if(p1.getId().equals(pdb.getId()))
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178 if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
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179 seqs.addElement(ap.av.alignment.getSequenceAt(i));
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186 SequenceI [] seqs2 = new SequenceI[seqs.size()];
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187 seqs.toArray(seqs2);
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189 new AppJMol(pdb, seqs2, ap);
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192 viewStructureMenu.add(menuItem);
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194 menuItem = new JMenuItem();
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195 menuItem.setText(pdb.getId());
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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 colourByStructure(pdb.getId());
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203 colStructureMenu.add(menuItem);
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207 menuItem = new JMenuItem("Hide Sequences");
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208 menuItem.addActionListener(new java.awt.event.ActionListener()
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210 public void actionPerformed(ActionEvent e)
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212 hideSequences(false);
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217 if (ap.av.getSelectionGroup() != null
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218 && ap.av.getSelectionGroup().getSize() > 1)
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220 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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221 menuItem.addActionListener(new java.awt.event.ActionListener()
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223 public void actionPerformed(ActionEvent e)
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225 hideSequences(true);
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228 sequenceMenu.add(menuItem);
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231 if (ap.av.hasHiddenRows)
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233 final int index = ap.av.alignment.findIndex(seq);
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235 if (ap.av.adjustForHiddenSeqs(index) -
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236 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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238 menuItem = new JMenuItem("Reveal Sequences");
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239 menuItem.addActionListener(new ActionListener()
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241 public void actionPerformed(ActionEvent e)
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243 ap.av.showSequence(index);
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244 if (ap.overviewPanel != null)
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246 ap.overviewPanel.updateOverviewImage();
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253 menuItem = new JMenuItem("Reveal All");
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254 menuItem.addActionListener(new ActionListener()
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256 public void actionPerformed(ActionEvent e)
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258 ap.av.showAllHiddenSeqs();
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259 if (ap.overviewPanel != null)
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261 ap.overviewPanel.updateOverviewImage();
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271 SequenceGroup sg = ap.av.getSelectionGroup();
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275 groupName.setText(sg.getName());
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277 if (sg.cs instanceof ZappoColourScheme)
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279 zappoColour.setSelected(true);
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281 else if (sg.cs instanceof TaylorColourScheme)
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283 taylorColour.setSelected(true);
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285 else if (sg.cs instanceof PIDColourScheme)
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287 PIDColour.setSelected(true);
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289 else if (sg.cs instanceof Blosum62ColourScheme)
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291 BLOSUM62Colour.setSelected(true);
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293 else if (sg.cs instanceof UserColourScheme)
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295 userDefinedColour.setSelected(true);
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297 else if (sg.cs instanceof HydrophobicColourScheme)
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299 hydrophobicityColour.setSelected(true);
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301 else if (sg.cs instanceof HelixColourScheme)
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303 helixColour.setSelected(true);
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305 else if (sg.cs instanceof StrandColourScheme)
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307 strandColour.setSelected(true);
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309 else if (sg.cs instanceof TurnColourScheme)
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311 turnColour.setSelected(true);
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313 else if (sg.cs instanceof BuriedColourScheme)
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315 buriedColour.setSelected(true);
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317 else if (sg.cs instanceof ClustalxColourScheme)
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319 clustalColour.setSelected(true);
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323 noColourmenuItem.setSelected(true);
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326 if (sg.cs != null && sg.cs.conservationApplied())
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328 conservationMenuItem.setSelected(true);
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331 showText.setSelected(sg.getDisplayText());
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332 showColourText.setSelected(sg.getColourText());
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333 showBoxes.setSelected(sg.getDisplayBoxes());
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337 groupMenu.setVisible(false);
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338 editMenu.setVisible(false);
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341 if (!ap.av.alignment.getGroups().contains(sg))
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343 unGroupMenuItem.setVisible(false);
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348 sequenceMenu.setVisible(false);
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349 structureMenu.setVisible(false);
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352 if (links != null && links.size() > 0)
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354 JMenu linkMenu = new JMenu("Link");
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356 for (int i = 0; i < links.size(); i++)
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358 String link = links.elementAt(i).toString();
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359 final String label = link.substring(0, link.indexOf("|"));
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360 item = new JMenuItem(label);
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363 if (link.indexOf("$SEQUENCE_ID$") > -1)
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365 String id = seq.getName();
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366 if (id.indexOf("|") > -1)
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368 id = id.substring(id.lastIndexOf("|") + 1);
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371 url = link.substring(link.indexOf("|") + 1,
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372 link.indexOf("$SEQUENCE_ID$"))
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374 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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378 url = link.substring(link.lastIndexOf("|") + 1);
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381 item.addActionListener(new java.awt.event.ActionListener()
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383 public void actionPerformed(ActionEvent e)
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389 linkMenu.add(item);
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391 if (sequence != null)
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393 sequenceMenu.add(linkMenu);
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405 * @throws Exception DOCUMENT ME!
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407 private void jbInit()
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410 groupMenu.setText("Group");
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411 groupMenu.setText("Selection");
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412 groupName.setText("Name");
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413 groupName.addActionListener(new java.awt.event.ActionListener()
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415 public void actionPerformed(ActionEvent e)
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417 groupName_actionPerformed();
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420 sequenceMenu.setText("Sequence");
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421 sequenceName.setText("Edit Name/Description");
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422 sequenceName.addActionListener(new java.awt.event.ActionListener()
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424 public void actionPerformed(ActionEvent e)
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426 sequenceName_actionPerformed();
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429 PIDColour.setFocusPainted(false);
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430 unGroupMenuItem.setText("Remove Group");
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431 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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433 public void actionPerformed(ActionEvent e)
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435 unGroupMenuItem_actionPerformed();
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439 outline.setText("Border colour");
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440 outline.addActionListener(new java.awt.event.ActionListener()
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442 public void actionPerformed(ActionEvent e)
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444 outline_actionPerformed();
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447 nucleotideMenuItem.setText("Nucleotide");
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448 nucleotideMenuItem.addActionListener(new ActionListener()
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450 public void actionPerformed(ActionEvent e)
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452 nucleotideMenuItem_actionPerformed();
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455 colourMenu.setText("Group Colour");
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456 showBoxes.setText("Boxes");
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457 showBoxes.setState(true);
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458 showBoxes.addActionListener(new ActionListener()
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460 public void actionPerformed(ActionEvent e)
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462 showBoxes_actionPerformed();
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465 showText.setText("Text");
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466 showText.setState(true);
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467 showText.addActionListener(new ActionListener()
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469 public void actionPerformed(ActionEvent e)
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471 showText_actionPerformed();
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474 showColourText.setText("Colour Text");
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475 showColourText.addActionListener(new ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 showColourText_actionPerformed();
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482 editMenu.setText("Edit");
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483 cut.setText("Cut");
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484 cut.addActionListener(new ActionListener()
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486 public void actionPerformed(ActionEvent e)
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488 cut_actionPerformed();
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491 upperCase.setText("To Upper Case");
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492 upperCase.addActionListener(new ActionListener()
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494 public void actionPerformed(ActionEvent e)
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499 copy.setText("Copy");
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500 copy.addActionListener(new ActionListener()
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502 public void actionPerformed(ActionEvent e)
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504 copy_actionPerformed();
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507 lowerCase.setText("To Lower Case");
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508 lowerCase.addActionListener(new ActionListener()
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510 public void actionPerformed(ActionEvent e)
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515 toggle.setText("Toggle Case");
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516 toggle.addActionListener(new ActionListener()
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518 public void actionPerformed(ActionEvent e)
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523 pdbMenu.setText("Associate Structure with Sequence");
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524 pdbFromFile.setText("From File");
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525 pdbFromFile.addActionListener(new ActionListener()
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527 public void actionPerformed(ActionEvent e)
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529 pdbFromFile_actionPerformed();
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532 enterPDB.setText("Enter PDB Id");
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533 enterPDB.addActionListener(new ActionListener()
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535 public void actionPerformed(ActionEvent e)
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537 enterPDB_actionPerformed();
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540 discoverPDB.setText("Discover PDB ids");
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541 discoverPDB.addActionListener(new ActionListener()
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543 public void actionPerformed(ActionEvent e)
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545 discoverPDB_actionPerformed();
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548 outputMenu.setText("Output to Textbox...");
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549 sequenceFeature.setText("Create Sequence Feature");
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550 sequenceFeature.addActionListener(new ActionListener()
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552 public void actionPerformed(ActionEvent e)
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554 sequenceFeature_actionPerformed();
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557 textColour.setText("Text Colour");
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558 textColour.addActionListener(new ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 textColour_actionPerformed();
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565 jMenu1.setText("Group");
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566 structureMenu.setText("Structure");
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567 viewStructureMenu.setText("View Structure");
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568 colStructureMenu.setText("Colour By Structure");
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573 this.add(structureMenu);
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574 groupMenu.add(editMenu);
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575 groupMenu.add(outputMenu);
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576 groupMenu.add(sequenceFeature);
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577 groupMenu.add(jMenu1);
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578 sequenceMenu.add(sequenceName);
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579 colourMenu.add(textColour);
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580 colourMenu.add(noColourmenuItem);
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581 colourMenu.add(clustalColour);
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582 colourMenu.add(BLOSUM62Colour);
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583 colourMenu.add(PIDColour);
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584 colourMenu.add(zappoColour);
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585 colourMenu.add(taylorColour);
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586 colourMenu.add(hydrophobicityColour);
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587 colourMenu.add(helixColour);
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588 colourMenu.add(strandColour);
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589 colourMenu.add(turnColour);
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590 colourMenu.add(buriedColour);
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591 colourMenu.add(nucleotideMenuItem);
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592 colourMenu.add(userDefinedColour);
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594 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
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596 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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597 getUserColourSchemes().keys();
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599 while (userColours.hasMoreElements())
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601 JMenuItem item = new JMenuItem(userColours.
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602 nextElement().toString());
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603 item.addActionListener(new ActionListener()
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605 public void actionPerformed(ActionEvent evt)
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607 userDefinedColour_actionPerformed(evt);
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610 colourMenu.add(item);
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614 colourMenu.addSeparator();
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615 colourMenu.add(abovePIDColour);
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616 colourMenu.add(conservationMenuItem);
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617 editMenu.add(copy);
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619 editMenu.add(upperCase);
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620 editMenu.add(lowerCase);
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621 editMenu.add(toggle);
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622 pdbMenu.add(pdbFromFile);
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623 pdbMenu.add(enterPDB);
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624 pdbMenu.add(discoverPDB);
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625 jMenu1.add(groupName);
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626 jMenu1.add(unGroupMenuItem);
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627 jMenu1.add(colourMenu);
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628 jMenu1.add(showBoxes);
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629 jMenu1.add(showText);
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630 jMenu1.add(showColourText);
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631 jMenu1.add(outline);
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632 structureMenu.add(pdbMenu);
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633 structureMenu.add(viewStructureMenu);
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634 structureMenu.add(colStructureMenu);
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635 noColourmenuItem.setText("None");
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636 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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638 public void actionPerformed(ActionEvent e)
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640 noColourmenuItem_actionPerformed();
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644 clustalColour.setText("Clustalx colours");
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645 clustalColour.addActionListener(new java.awt.event.ActionListener()
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647 public void actionPerformed(ActionEvent e)
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649 clustalColour_actionPerformed();
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652 zappoColour.setText("Zappo");
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653 zappoColour.addActionListener(new java.awt.event.ActionListener()
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655 public void actionPerformed(ActionEvent e)
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657 zappoColour_actionPerformed();
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660 taylorColour.setText("Taylor");
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661 taylorColour.addActionListener(new java.awt.event.ActionListener()
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663 public void actionPerformed(ActionEvent e)
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665 taylorColour_actionPerformed();
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668 hydrophobicityColour.setText("Hydrophobicity");
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669 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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671 public void actionPerformed(ActionEvent e)
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673 hydrophobicityColour_actionPerformed();
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676 helixColour.setText("Helix propensity");
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677 helixColour.addActionListener(new java.awt.event.ActionListener()
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679 public void actionPerformed(ActionEvent e)
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681 helixColour_actionPerformed();
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684 strandColour.setText("Strand propensity");
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685 strandColour.addActionListener(new java.awt.event.ActionListener()
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687 public void actionPerformed(ActionEvent e)
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689 strandColour_actionPerformed();
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692 turnColour.setText("Turn propensity");
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693 turnColour.addActionListener(new java.awt.event.ActionListener()
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695 public void actionPerformed(ActionEvent e)
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697 turnColour_actionPerformed();
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700 buriedColour.setText("Buried Index");
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701 buriedColour.addActionListener(new java.awt.event.ActionListener()
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703 public void actionPerformed(ActionEvent e)
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705 buriedColour_actionPerformed();
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708 abovePIDColour.setText("Above % Identity");
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709 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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711 public void actionPerformed(ActionEvent e)
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713 abovePIDColour_actionPerformed();
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716 userDefinedColour.setText("User Defined...");
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717 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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719 public void actionPerformed(ActionEvent e)
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721 userDefinedColour_actionPerformed(e);
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724 PIDColour.setText("Percentage Identity");
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725 PIDColour.addActionListener(new java.awt.event.ActionListener()
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727 public void actionPerformed(ActionEvent e)
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729 PIDColour_actionPerformed();
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732 BLOSUM62Colour.setText("BLOSUM62");
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733 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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735 public void actionPerformed(ActionEvent e)
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737 BLOSUM62Colour_actionPerformed();
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740 conservationMenuItem.setText("Conservation");
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741 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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743 public void actionPerformed(ActionEvent e)
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745 conservationMenuItem_actionPerformed();
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755 ap.paintAlignment(true);
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757 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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763 * @param e DOCUMENT ME!
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765 protected void clustalColour_actionPerformed()
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767 SequenceGroup sg = getGroup();
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768 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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769 ap.av.alignment.getWidth());
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776 * @param e DOCUMENT ME!
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778 protected void zappoColour_actionPerformed()
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780 getGroup().cs = new ZappoColourScheme();
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787 * @param e DOCUMENT ME!
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789 protected void taylorColour_actionPerformed()
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791 getGroup().cs = new TaylorColourScheme();
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798 * @param e DOCUMENT ME!
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800 protected void hydrophobicityColour_actionPerformed()
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802 getGroup().cs = new HydrophobicColourScheme();
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809 * @param e DOCUMENT ME!
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811 protected void helixColour_actionPerformed()
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813 getGroup().cs = new HelixColourScheme();
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820 * @param e DOCUMENT ME!
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822 protected void strandColour_actionPerformed()
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824 getGroup().cs = new StrandColourScheme();
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831 * @param e DOCUMENT ME!
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833 protected void turnColour_actionPerformed()
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835 getGroup().cs = new TurnColourScheme();
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842 * @param e DOCUMENT ME!
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844 protected void buriedColour_actionPerformed()
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846 getGroup().cs = new BuriedColourScheme();
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853 * @param e DOCUMENT ME!
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855 public void nucleotideMenuItem_actionPerformed()
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857 getGroup().cs = new NucleotideColourScheme();
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864 * @param e DOCUMENT ME!
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866 protected void abovePIDColour_actionPerformed()
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868 SequenceGroup sg = getGroup();
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874 if (abovePIDColour.isSelected())
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876 sg.cs.setConsensus(AAFrequency.calculate(
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877 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
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878 sg.getEndRes() + 1));
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880 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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881 getGroup().getName());
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883 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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885 SliderPanel.showPIDSlider();
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887 else // remove PIDColouring
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889 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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898 * @param e DOCUMENT ME!
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900 protected void userDefinedColour_actionPerformed(ActionEvent e)
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902 SequenceGroup sg = getGroup();
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904 if (e.getActionCommand().equals("User Defined..."))
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906 new UserDefinedColours(ap, sg);
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910 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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911 getUserColourSchemes().get(e.getActionCommand());
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921 * @param e DOCUMENT ME!
\r
923 protected void PIDColour_actionPerformed()
\r
925 SequenceGroup sg = getGroup();
\r
926 sg.cs = new PIDColourScheme();
\r
927 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
928 hiddenRepSequences),
\r
930 sg.getEndRes() + 1));
\r
937 * @param e DOCUMENT ME!
\r
939 protected void BLOSUM62Colour_actionPerformed()
\r
941 SequenceGroup sg = getGroup();
\r
943 sg.cs = new Blosum62ColourScheme();
\r
945 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
946 hiddenRepSequences),
\r
948 sg.getEndRes() + 1));
\r
956 * @param e DOCUMENT ME!
\r
958 protected void noColourmenuItem_actionPerformed()
\r
960 getGroup().cs = null;
\r
967 * @param e DOCUMENT ME!
\r
969 protected void conservationMenuItem_actionPerformed()
\r
971 SequenceGroup sg = getGroup();
\r
977 if (conservationMenuItem.isSelected())
\r
979 Conservation c = new Conservation("Group",
\r
980 ResidueProperties.propHash, 3,
\r
981 sg.getSequences(ap.av.
\r
982 hiddenRepSequences),
\r
984 sg.getEndRes() + 1);
\r
987 c.verdict(false, ap.av.ConsPercGaps);
\r
989 sg.cs.setConservation(c);
\r
991 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
992 SliderPanel.showConservationSlider();
\r
994 else // remove ConservationColouring
\r
996 sg.cs.setConservation(null);
\r
1005 * @param e DOCUMENT ME!
\r
1007 protected void groupName_actionPerformed()
\r
1010 SequenceGroup sg = getGroup();
\r
1011 EditNameDialog dialog = new EditNameDialog(sg.getName(),
\r
1012 sg.getDescription(),
\r
1014 "Group Description ",
\r
1015 "Edit Group Name/Description");
\r
1017 if (!dialog.accept)
\r
1022 sg.setName(dialog.getName());
\r
1023 sg.setDescription(dialog.getDescription());
\r
1029 * @return DOCUMENT ME!
\r
1031 SequenceGroup getGroup()
\r
1033 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1034 // this method won't add a new group if it already exists
\r
1037 ap.av.alignment.addGroup(sg);
\r
1046 * @param e DOCUMENT ME!
\r
1048 void sequenceName_actionPerformed()
\r
1050 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
\r
1051 sequence.getDescription(),
\r
1052 " Sequence Name ",
\r
1053 "Sequence Description ",
\r
1054 "Edit Sequence Name/Description");
\r
1056 if (!dialog.accept)
\r
1061 if (dialog.getName() != null)
\r
1063 if (dialog.getName().indexOf(" ") > -1)
\r
1065 JOptionPane.showMessageDialog(ap,
\r
1066 "Spaces have been converted to \"_\"",
\r
1067 "No spaces allowed in Sequence Name",
\r
1068 JOptionPane.WARNING_MESSAGE);
\r
1071 sequence.setName(dialog.getName().replace(' ', '_'));
\r
1072 ap.paintAlignment(false);
\r
1075 sequence.setDescription(dialog.getDescription());
\r
1077 ap.av.firePropertyChange("alignment", null,
\r
1078 ap.av.getAlignment().getSequences());
\r
1085 * @param e DOCUMENT ME!
\r
1087 void unGroupMenuItem_actionPerformed()
\r
1089 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1090 ap.av.alignment.deleteGroup(sg);
\r
1091 ap.av.setSelectionGroup(null);
\r
1098 * @param e DOCUMENT ME!
\r
1100 protected void outline_actionPerformed()
\r
1102 SequenceGroup sg = getGroup();
\r
1103 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1108 sg.setOutlineColour(col);
\r
1117 * @param e DOCUMENT ME!
\r
1119 public void showBoxes_actionPerformed()
\r
1121 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1128 * @param e DOCUMENT ME!
\r
1130 public void showText_actionPerformed()
\r
1132 getGroup().setDisplayText(showText.isSelected());
\r
1139 * @param e DOCUMENT ME!
\r
1141 public void showColourText_actionPerformed()
\r
1143 getGroup().setColourText(showColourText.isSelected());
\r
1147 public void showLink(String url)
\r
1151 jalview.util.BrowserLauncher.openURL(url);
\r
1153 catch (Exception ex)
\r
1155 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1156 "Unixers: Couldn't find default web browser."
\r
1158 "\nAdd the full path to your browser in Preferences.",
\r
1159 "Web browser not found",
\r
1160 JOptionPane.WARNING_MESSAGE);
\r
1162 ex.printStackTrace();
\r
1166 void hideSequences(boolean representGroup)
\r
1168 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1169 if (sg == null || sg.getSize() < 1)
\r
1171 ap.av.hideSequence(new SequenceI[]
\r
1176 ap.av.setSelectionGroup(null);
\r
1178 if (representGroup)
\r
1180 ap.av.hideRepSequences(sequence, sg);
\r
1185 int gsize = sg.getSize();
\r
1186 SequenceI[] hseqs;
\r
1188 hseqs = new SequenceI[gsize];
\r
1191 for (int i = 0; i < gsize; i++)
\r
1193 hseqs[index++] = sg.getSequenceAt(i);
\r
1196 ap.av.hideSequence(hseqs);
\r
1199 public void copy_actionPerformed()
\r
1201 ap.alignFrame.copy_actionPerformed(null);
\r
1204 public void cut_actionPerformed()
\r
1206 ap.alignFrame.cut_actionPerformed(null);
\r
1209 void changeCase(ActionEvent e)
\r
1211 Object source = e.getSource();
\r
1212 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1216 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
\r
1217 sg.getStartRes(), sg.getEndRes() + 1);
\r
1219 String description;
\r
1222 if (source == toggle)
\r
1224 description = "Toggle Case";
\r
1225 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1227 else if (source == upperCase)
\r
1229 description = "To Upper Case";
\r
1230 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1234 description = "To Lower Case";
\r
1235 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1238 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1239 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1240 startEnd, caseChange
\r
1243 ap.alignFrame.addHistoryItem(caseCommand);
\r
1245 ap.av.firePropertyChange("alignment", null,
\r
1246 ap.av.getAlignment().getSequences());
\r
1251 public void outputText_actionPerformed(ActionEvent e)
\r
1253 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1254 cap.setForInput(null);
\r
1255 Desktop.addInternalFrame(cap,
\r
1256 "Alignment output - " + e.getActionCommand(), 600,
\r
1259 String[] omitHidden = null;
\r
1261 if (ap.av.hasHiddenColumns)
\r
1263 System.out.println("PROMPT USER HERE");
\r
1264 omitHidden = ap.av.getViewAsString(true);
\r
1267 cap.setText(new FormatAdapter().formatSequences(
\r
1268 e.getActionCommand(),
\r
1269 ap.av.getSelectionAsNewSequence(),
\r
1273 public void pdbFromFile_actionPerformed()
\r
1275 jalview.io.JalviewFileChooser chooser
\r
1276 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1278 "LAST_DIRECTORY"));
\r
1279 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1280 chooser.setDialogTitle("Select a PDB file");
\r
1281 chooser.setToolTipText("Load a PDB file");
\r
1283 int value = chooser.showOpenDialog(null);
\r
1285 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1287 PDBEntry entry = new PDBEntry();
\r
1288 String choice = chooser.getSelectedFile().getPath();
\r
1289 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1292 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1293 jalview.io.AppletFormatAdapter.FILE);
\r
1295 if (pdbfile.id == null)
\r
1297 String reply = JOptionPane.showInternalInputDialog(
\r
1299 "Couldn't find a PDB id in the file supplied."
\r
1300 + "Please enter an Id to identify this structure.",
\r
1301 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1302 if (reply == null)
\r
1307 entry.setId(reply);
\r
1311 entry.setId(pdbfile.id);
\r
1314 catch (java.io.IOException ex)
\r
1316 ex.printStackTrace();
\r
1319 entry.setFile(choice);
\r
1320 sequence.getDatasetSequence().addPDBId(entry);
\r
1325 public void enterPDB_actionPerformed()
\r
1327 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1328 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1330 if (id != null && id.length() > 0)
\r
1332 PDBEntry entry = new PDBEntry();
\r
1334 sequence.getDatasetSequence()
\r
1339 public void discoverPDB_actionPerformed()
\r
1341 SequenceI[] sequences =
\r
1342 ap.av.selectionGroup == null ?
\r
1343 new Sequence[]{sequence}
\r
1344 : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
\r
1346 new jalview.io.DBRefFetcher(sequences,
\r
1347 ap.alignFrame).fetchDBRefs(false);
\r
1350 public void sequenceFeature_actionPerformed()
\r
1352 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1358 int gSize = sg.getSize();
\r
1359 SequenceI[] seqs = new SequenceI[gSize];
\r
1360 SequenceFeature[] features = new SequenceFeature[gSize];
\r
1362 for (int i = 0; i < gSize; i++)
\r
1364 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1365 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1366 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1367 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
\r
1370 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1371 .amendFeatures(seqs, features, true, ap))
\r
1373 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1374 ap.av.setShowSequenceFeatures(true);
\r
1375 ap.highlightSearchResults(null);
\r
1379 public void textColour_actionPerformed()
\r
1381 SequenceGroup sg = getGroup();
\r
1384 new TextColourChooser().chooseColour(ap, sg);
\r
1388 public void colourByStructure(String pdbid)
\r
1390 Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
\r
1391 .colourSequenceFromStructure(sequence, pdbid);
\r
1393 AlignmentAnnotation an = new AlignmentAnnotation(
\r
1394 "Structure", "Coloured by "+pdbid, anots);
\r
1396 ap.av.alignment.addAnnotation(an);
\r
1397 an.createSequenceMapping(sequence, 0, true);
\r
1398 //an.adjustForAlignment();
\r
1399 ap.av.alignment.setAnnotationIndex(an,0);
\r
1401 ap.adjustAnnotationHeight();
\r
1403 sequence.addAlignmentAnnotation(an);
\r