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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88 JMenuItem editSequence = new JMenuItem();
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89 // JMenuItem annotationMenuItem = new JMenuItem();
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92 * Creates a new PopupMenu object.
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94 * @param ap DOCUMENT ME!
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95 * @param seq DOCUMENT ME!
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97 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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99 ///////////////////////////////////////////////////////////
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100 // If this is activated from the sequence panel, the user may want to
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101 // edit or annotate a particular residue. Therefore display the residue menu
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103 // If from the IDPanel, we must display the sequence menu
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104 //////////////////////////////////////////////////////////
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108 ButtonGroup colours = new ButtonGroup();
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109 colours.add(noColourmenuItem);
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110 colours.add(clustalColour);
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111 colours.add(zappoColour);
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112 colours.add(taylorColour);
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113 colours.add(hydrophobicityColour);
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114 colours.add(helixColour);
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115 colours.add(strandColour);
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116 colours.add(turnColour);
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117 colours.add(buriedColour);
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118 colours.add(abovePIDColour);
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119 colours.add(userDefinedColour);
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120 colours.add(PIDColour);
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121 colours.add(BLOSUM62Colour);
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123 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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125 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
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128 item.addActionListener(new java.awt.event.ActionListener()
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130 public void actionPerformed(ActionEvent e)
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132 outputText_actionPerformed(e);
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136 outputMenu.add(item);
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143 catch (Exception e)
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145 e.printStackTrace();
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150 sequenceMenu.setText(sequence.getName());
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152 JMenuItem menuItem;
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153 if (seq.getDatasetSequence().getPDBId() != null
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154 && seq.getDatasetSequence().getPDBId().size()>0)
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156 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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159 while (e.hasMoreElements())
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161 final PDBEntry pdb = (PDBEntry) e.nextElement();
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163 menuItem = new JMenuItem();
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164 menuItem.setText(pdb.getId());
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165 menuItem.addActionListener(new java.awt.event.ActionListener()
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167 public void actionPerformed(ActionEvent e)
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169 Vector seqs = new Vector();
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170 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
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172 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
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176 for(int p=0; p<pdbs.size(); p++)
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178 PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
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179 if(p1.getId().equals(pdb.getId()))
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181 if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
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182 seqs.addElement(ap.av.alignment.getSequenceAt(i));
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189 SequenceI [] seqs2 = new SequenceI[seqs.size()];
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190 seqs.toArray(seqs2);
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192 new AppJMol(pdb, seqs2, null, ap);
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195 viewStructureMenu.add(menuItem);
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197 /* menuItem = new JMenuItem();
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198 menuItem.setText(pdb.getId());
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199 menuItem.addActionListener(new java.awt.event.ActionListener()
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201 public void actionPerformed(ActionEvent e)
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203 colourByStructure(pdb.getId());
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206 colStructureMenu.add(menuItem);*/
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211 structureMenu.remove(viewStructureMenu);
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212 // structureMenu.remove(colStructureMenu);
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215 menuItem = new JMenuItem("Hide Sequences");
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216 menuItem.addActionListener(new java.awt.event.ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 hideSequences(false);
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225 if (ap.av.getSelectionGroup() != null
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226 && ap.av.getSelectionGroup().getSize() > 1)
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228 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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229 menuItem.addActionListener(new java.awt.event.ActionListener()
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231 public void actionPerformed(ActionEvent e)
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233 hideSequences(true);
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236 sequenceMenu.add(menuItem);
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239 if (ap.av.hasHiddenRows)
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241 final int index = ap.av.alignment.findIndex(seq);
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243 if (ap.av.adjustForHiddenSeqs(index) -
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244 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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246 menuItem = new JMenuItem("Reveal Sequences");
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247 menuItem.addActionListener(new ActionListener()
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249 public void actionPerformed(ActionEvent e)
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251 ap.av.showSequence(index);
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252 if (ap.overviewPanel != null)
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254 ap.overviewPanel.updateOverviewImage();
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261 menuItem = new JMenuItem("Reveal All");
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262 menuItem.addActionListener(new ActionListener()
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264 public void actionPerformed(ActionEvent e)
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266 ap.av.showAllHiddenSeqs();
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267 if (ap.overviewPanel != null)
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269 ap.overviewPanel.updateOverviewImage();
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279 SequenceGroup sg = ap.av.getSelectionGroup();
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283 groupName.setText(sg.getName());
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285 if (sg.cs instanceof ZappoColourScheme)
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287 zappoColour.setSelected(true);
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289 else if (sg.cs instanceof TaylorColourScheme)
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291 taylorColour.setSelected(true);
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293 else if (sg.cs instanceof PIDColourScheme)
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295 PIDColour.setSelected(true);
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297 else if (sg.cs instanceof Blosum62ColourScheme)
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299 BLOSUM62Colour.setSelected(true);
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301 else if (sg.cs instanceof UserColourScheme)
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303 userDefinedColour.setSelected(true);
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305 else if (sg.cs instanceof HydrophobicColourScheme)
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307 hydrophobicityColour.setSelected(true);
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309 else if (sg.cs instanceof HelixColourScheme)
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311 helixColour.setSelected(true);
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313 else if (sg.cs instanceof StrandColourScheme)
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315 strandColour.setSelected(true);
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317 else if (sg.cs instanceof TurnColourScheme)
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319 turnColour.setSelected(true);
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321 else if (sg.cs instanceof BuriedColourScheme)
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323 buriedColour.setSelected(true);
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325 else if (sg.cs instanceof ClustalxColourScheme)
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327 clustalColour.setSelected(true);
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331 noColourmenuItem.setSelected(true);
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334 if (sg.cs != null && sg.cs.conservationApplied())
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336 conservationMenuItem.setSelected(true);
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339 showText.setSelected(sg.getDisplayText());
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340 showColourText.setSelected(sg.getColourText());
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341 showBoxes.setSelected(sg.getDisplayBoxes());
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345 groupMenu.setVisible(false);
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346 editMenu.setVisible(false);
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349 if (!ap.av.alignment.getGroups().contains(sg))
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351 unGroupMenuItem.setVisible(false);
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356 sequenceMenu.setVisible(false);
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357 structureMenu.setVisible(false);
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360 if (links != null && links.size() > 0)
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362 JMenu linkMenu = new JMenu("Link");
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364 for (int i = 0; i < links.size(); i++)
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366 String link = links.elementAt(i).toString();
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367 final String label = link.substring(0, link.indexOf("|"));
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368 item = new JMenuItem(label);
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371 if (link.indexOf("$SEQUENCE_ID$") > -1)
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373 String id = seq.getName();
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374 if (id.indexOf("|") > -1)
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376 id = id.substring(id.lastIndexOf("|") + 1);
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379 url = link.substring(link.indexOf("|") + 1,
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380 link.indexOf("$SEQUENCE_ID$"))
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382 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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386 url = link.substring(link.lastIndexOf("|") + 1);
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389 item.addActionListener(new java.awt.event.ActionListener()
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391 public void actionPerformed(ActionEvent e)
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397 linkMenu.add(item);
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399 if (sequence != null)
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401 sequenceMenu.add(linkMenu);
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413 * @throws Exception DOCUMENT ME!
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415 private void jbInit()
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418 groupMenu.setText("Group");
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419 groupMenu.setText("Selection");
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420 groupName.setText("Name");
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421 groupName.addActionListener(new java.awt.event.ActionListener()
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423 public void actionPerformed(ActionEvent e)
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425 groupName_actionPerformed();
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428 sequenceMenu.setText("Sequence");
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429 sequenceName.setText("Edit Name/Description");
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430 sequenceName.addActionListener(new java.awt.event.ActionListener()
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432 public void actionPerformed(ActionEvent e)
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434 sequenceName_actionPerformed();
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437 PIDColour.setFocusPainted(false);
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438 unGroupMenuItem.setText("Remove Group");
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439 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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441 public void actionPerformed(ActionEvent e)
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443 unGroupMenuItem_actionPerformed();
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447 outline.setText("Border colour");
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448 outline.addActionListener(new java.awt.event.ActionListener()
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450 public void actionPerformed(ActionEvent e)
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452 outline_actionPerformed();
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455 nucleotideMenuItem.setText("Nucleotide");
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456 nucleotideMenuItem.addActionListener(new ActionListener()
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458 public void actionPerformed(ActionEvent e)
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460 nucleotideMenuItem_actionPerformed();
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463 colourMenu.setText("Group Colour");
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464 showBoxes.setText("Boxes");
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465 showBoxes.setState(true);
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466 showBoxes.addActionListener(new ActionListener()
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468 public void actionPerformed(ActionEvent e)
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470 showBoxes_actionPerformed();
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473 showText.setText("Text");
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474 showText.setState(true);
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475 showText.addActionListener(new ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 showText_actionPerformed();
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482 showColourText.setText("Colour Text");
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483 showColourText.addActionListener(new ActionListener()
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485 public void actionPerformed(ActionEvent e)
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487 showColourText_actionPerformed();
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490 editMenu.setText("Edit");
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491 cut.setText("Cut");
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492 cut.addActionListener(new ActionListener()
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494 public void actionPerformed(ActionEvent e)
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496 cut_actionPerformed();
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499 upperCase.setText("To Upper Case");
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500 upperCase.addActionListener(new ActionListener()
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502 public void actionPerformed(ActionEvent e)
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507 copy.setText("Copy");
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508 copy.addActionListener(new ActionListener()
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510 public void actionPerformed(ActionEvent e)
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512 copy_actionPerformed();
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515 lowerCase.setText("To Lower Case");
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516 lowerCase.addActionListener(new ActionListener()
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518 public void actionPerformed(ActionEvent e)
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523 toggle.setText("Toggle Case");
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524 toggle.addActionListener(new ActionListener()
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526 public void actionPerformed(ActionEvent e)
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531 pdbMenu.setText("Associate Structure with Sequence");
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532 pdbFromFile.setText("From File");
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533 pdbFromFile.addActionListener(new ActionListener()
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535 public void actionPerformed(ActionEvent e)
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537 pdbFromFile_actionPerformed();
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540 enterPDB.setText("Enter PDB Id");
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541 enterPDB.addActionListener(new ActionListener()
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543 public void actionPerformed(ActionEvent e)
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545 enterPDB_actionPerformed();
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548 discoverPDB.setText("Discover PDB ids");
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549 discoverPDB.addActionListener(new ActionListener()
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551 public void actionPerformed(ActionEvent e)
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553 discoverPDB_actionPerformed();
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556 outputMenu.setText("Output to Textbox...");
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557 sequenceFeature.setText("Create Sequence Feature");
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558 sequenceFeature.addActionListener(new ActionListener()
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560 public void actionPerformed(ActionEvent e)
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562 sequenceFeature_actionPerformed();
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565 textColour.setText("Text Colour");
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566 textColour.addActionListener(new ActionListener()
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568 public void actionPerformed(ActionEvent e)
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570 textColour_actionPerformed();
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573 jMenu1.setText("Group");
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574 structureMenu.setText("Structure");
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575 viewStructureMenu.setText("View Structure");
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576 // colStructureMenu.setText("Colour By Structure");
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577 editSequence.setText("Edit Sequence...");
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578 editSequence.addActionListener(new ActionListener()
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580 public void actionPerformed(ActionEvent actionEvent)
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582 editSequence_actionPerformed(actionEvent);
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585 /* annotationMenuItem.setText("By Annotation");
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586 annotationMenuItem.addActionListener(new ActionListener()
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588 public void actionPerformed(ActionEvent actionEvent)
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590 annotationMenuItem_actionPerformed(actionEvent);
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597 this.add(structureMenu);
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598 groupMenu.add(editMenu);
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599 groupMenu.add(outputMenu);
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600 groupMenu.add(sequenceFeature);
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601 groupMenu.add(jMenu1);
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602 sequenceMenu.add(sequenceName);
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603 colourMenu.add(textColour);
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604 colourMenu.add(noColourmenuItem);
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605 colourMenu.add(clustalColour);
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606 colourMenu.add(BLOSUM62Colour);
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607 colourMenu.add(PIDColour);
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608 colourMenu.add(zappoColour);
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609 colourMenu.add(taylorColour);
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610 colourMenu.add(hydrophobicityColour);
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611 colourMenu.add(helixColour);
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612 colourMenu.add(strandColour);
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613 colourMenu.add(turnColour);
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614 colourMenu.add(buriedColour);
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615 colourMenu.add(nucleotideMenuItem);
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616 colourMenu.add(userDefinedColour);
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618 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
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620 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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621 getUserColourSchemes().keys();
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623 while (userColours.hasMoreElements())
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625 JMenuItem item = new JMenuItem(userColours.
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626 nextElement().toString());
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627 item.addActionListener(new ActionListener()
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629 public void actionPerformed(ActionEvent evt)
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631 userDefinedColour_actionPerformed(evt);
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634 colourMenu.add(item);
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638 colourMenu.addSeparator();
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639 colourMenu.add(abovePIDColour);
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640 colourMenu.add(conservationMenuItem);
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641 //colourMenu.add(annotationMenuItem);
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642 editMenu.add(copy);
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644 editMenu.add(editSequence);
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645 editMenu.add(upperCase);
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646 editMenu.add(lowerCase);
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647 editMenu.add(toggle);
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648 pdbMenu.add(pdbFromFile);
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649 pdbMenu.add(enterPDB);
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650 pdbMenu.add(discoverPDB);
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651 jMenu1.add(groupName);
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652 jMenu1.add(unGroupMenuItem);
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653 jMenu1.add(colourMenu);
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654 jMenu1.add(showBoxes);
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655 jMenu1.add(showText);
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656 jMenu1.add(showColourText);
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657 jMenu1.add(outline);
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658 structureMenu.add(pdbMenu);
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659 structureMenu.add(viewStructureMenu);
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660 // structureMenu.add(colStructureMenu);
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661 noColourmenuItem.setText("None");
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662 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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664 public void actionPerformed(ActionEvent e)
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666 noColourmenuItem_actionPerformed();
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670 clustalColour.setText("Clustalx colours");
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671 clustalColour.addActionListener(new java.awt.event.ActionListener()
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673 public void actionPerformed(ActionEvent e)
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675 clustalColour_actionPerformed();
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678 zappoColour.setText("Zappo");
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679 zappoColour.addActionListener(new java.awt.event.ActionListener()
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681 public void actionPerformed(ActionEvent e)
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683 zappoColour_actionPerformed();
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686 taylorColour.setText("Taylor");
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687 taylorColour.addActionListener(new java.awt.event.ActionListener()
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689 public void actionPerformed(ActionEvent e)
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691 taylorColour_actionPerformed();
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694 hydrophobicityColour.setText("Hydrophobicity");
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695 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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697 public void actionPerformed(ActionEvent e)
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699 hydrophobicityColour_actionPerformed();
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702 helixColour.setText("Helix propensity");
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703 helixColour.addActionListener(new java.awt.event.ActionListener()
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705 public void actionPerformed(ActionEvent e)
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707 helixColour_actionPerformed();
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710 strandColour.setText("Strand propensity");
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711 strandColour.addActionListener(new java.awt.event.ActionListener()
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713 public void actionPerformed(ActionEvent e)
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715 strandColour_actionPerformed();
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718 turnColour.setText("Turn propensity");
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719 turnColour.addActionListener(new java.awt.event.ActionListener()
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721 public void actionPerformed(ActionEvent e)
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723 turnColour_actionPerformed();
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726 buriedColour.setText("Buried Index");
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727 buriedColour.addActionListener(new java.awt.event.ActionListener()
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729 public void actionPerformed(ActionEvent e)
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731 buriedColour_actionPerformed();
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734 abovePIDColour.setText("Above % Identity");
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735 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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737 public void actionPerformed(ActionEvent e)
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739 abovePIDColour_actionPerformed();
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742 userDefinedColour.setText("User Defined...");
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743 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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745 public void actionPerformed(ActionEvent e)
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747 userDefinedColour_actionPerformed(e);
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750 PIDColour.setText("Percentage Identity");
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751 PIDColour.addActionListener(new java.awt.event.ActionListener()
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753 public void actionPerformed(ActionEvent e)
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755 PIDColour_actionPerformed();
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758 BLOSUM62Colour.setText("BLOSUM62");
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759 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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761 public void actionPerformed(ActionEvent e)
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763 BLOSUM62Colour_actionPerformed();
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766 conservationMenuItem.setText("Conservation");
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767 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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769 public void actionPerformed(ActionEvent e)
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771 conservationMenuItem_actionPerformed();
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781 ap.paintAlignment(true);
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783 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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789 * @param e DOCUMENT ME!
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791 protected void clustalColour_actionPerformed()
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793 SequenceGroup sg = getGroup();
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794 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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795 ap.av.alignment.getWidth());
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802 * @param e DOCUMENT ME!
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804 protected void zappoColour_actionPerformed()
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806 getGroup().cs = new ZappoColourScheme();
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813 * @param e DOCUMENT ME!
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815 protected void taylorColour_actionPerformed()
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817 getGroup().cs = new TaylorColourScheme();
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824 * @param e DOCUMENT ME!
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826 protected void hydrophobicityColour_actionPerformed()
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828 getGroup().cs = new HydrophobicColourScheme();
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835 * @param e DOCUMENT ME!
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837 protected void helixColour_actionPerformed()
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839 getGroup().cs = new HelixColourScheme();
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846 * @param e DOCUMENT ME!
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848 protected void strandColour_actionPerformed()
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850 getGroup().cs = new StrandColourScheme();
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857 * @param e DOCUMENT ME!
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859 protected void turnColour_actionPerformed()
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861 getGroup().cs = new TurnColourScheme();
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868 * @param e DOCUMENT ME!
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870 protected void buriedColour_actionPerformed()
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872 getGroup().cs = new BuriedColourScheme();
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879 * @param e DOCUMENT ME!
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881 public void nucleotideMenuItem_actionPerformed()
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883 getGroup().cs = new NucleotideColourScheme();
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890 * @param e DOCUMENT ME!
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892 protected void abovePIDColour_actionPerformed()
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894 SequenceGroup sg = getGroup();
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900 if (abovePIDColour.isSelected())
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902 sg.cs.setConsensus(AAFrequency.calculate(
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903 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
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904 sg.getEndRes() + 1));
\r
906 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
907 getGroup().getName());
\r
909 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
\r
911 SliderPanel.showPIDSlider();
\r
913 else // remove PIDColouring
\r
915 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
924 * @param e DOCUMENT ME!
\r
926 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
928 SequenceGroup sg = getGroup();
\r
930 if (e.getActionCommand().equals("User Defined..."))
\r
932 new UserDefinedColours(ap, sg);
\r
936 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
937 getUserColourSchemes().get(e.getActionCommand());
\r
947 * @param e DOCUMENT ME!
\r
949 protected void PIDColour_actionPerformed()
\r
951 SequenceGroup sg = getGroup();
\r
952 sg.cs = new PIDColourScheme();
\r
953 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
954 hiddenRepSequences),
\r
956 sg.getEndRes() + 1));
\r
963 * @param e DOCUMENT ME!
\r
965 protected void BLOSUM62Colour_actionPerformed()
\r
967 SequenceGroup sg = getGroup();
\r
969 sg.cs = new Blosum62ColourScheme();
\r
971 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
972 hiddenRepSequences),
\r
974 sg.getEndRes() + 1));
\r
982 * @param e DOCUMENT ME!
\r
984 protected void noColourmenuItem_actionPerformed()
\r
986 getGroup().cs = null;
\r
993 * @param e DOCUMENT ME!
\r
995 protected void conservationMenuItem_actionPerformed()
\r
997 SequenceGroup sg = getGroup();
\r
1003 if (conservationMenuItem.isSelected())
\r
1005 Conservation c = new Conservation("Group",
\r
1006 ResidueProperties.propHash, 3,
\r
1007 sg.getSequences(ap.av.
\r
1008 hiddenRepSequences),
\r
1010 sg.getEndRes() + 1);
\r
1013 c.verdict(false, ap.av.ConsPercGaps);
\r
1015 sg.cs.setConservation(c);
\r
1017 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
1018 SliderPanel.showConservationSlider();
\r
1020 else // remove ConservationColouring
\r
1022 sg.cs.setConservation(null);
\r
1028 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
\r
1030 SequenceGroup sg = getGroup();
\r
1036 AnnotationColourGradient acg = new AnnotationColourGradient(
\r
1037 sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
\r
1039 acg.predefinedColours = true;
\r
1048 * @param e DOCUMENT ME!
\r
1050 protected void groupName_actionPerformed()
\r
1053 SequenceGroup sg = getGroup();
\r
1054 EditNameDialog dialog = new EditNameDialog(sg.getName(),
\r
1055 sg.getDescription(),
\r
1057 "Group Description ",
\r
1058 "Edit Group Name/Description");
\r
1060 if (!dialog.accept)
\r
1065 sg.setName(dialog.getName());
\r
1066 sg.setDescription(dialog.getDescription());
\r
1072 * @return DOCUMENT ME!
\r
1074 SequenceGroup getGroup()
\r
1076 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1077 // this method won't add a new group if it already exists
\r
1080 ap.av.alignment.addGroup(sg);
\r
1089 * @param e DOCUMENT ME!
\r
1091 void sequenceName_actionPerformed()
\r
1093 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
\r
1094 sequence.getDescription(),
\r
1095 " Sequence Name ",
\r
1096 "Sequence Description ",
\r
1097 "Edit Sequence Name/Description");
\r
1099 if (!dialog.accept)
\r
1104 if (dialog.getName() != null)
\r
1106 if (dialog.getName().indexOf(" ") > -1)
\r
1108 JOptionPane.showMessageDialog(ap,
\r
1109 "Spaces have been converted to \"_\"",
\r
1110 "No spaces allowed in Sequence Name",
\r
1111 JOptionPane.WARNING_MESSAGE);
\r
1114 sequence.setName(dialog.getName().replace(' ', '_'));
\r
1115 ap.paintAlignment(false);
\r
1118 sequence.setDescription(dialog.getDescription());
\r
1120 ap.av.firePropertyChange("alignment", null,
\r
1121 ap.av.getAlignment().getSequences());
\r
1128 * @param e DOCUMENT ME!
\r
1130 void unGroupMenuItem_actionPerformed()
\r
1132 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1133 ap.av.alignment.deleteGroup(sg);
\r
1134 ap.av.setSelectionGroup(null);
\r
1141 * @param e DOCUMENT ME!
\r
1143 protected void outline_actionPerformed()
\r
1145 SequenceGroup sg = getGroup();
\r
1146 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1151 sg.setOutlineColour(col);
\r
1160 * @param e DOCUMENT ME!
\r
1162 public void showBoxes_actionPerformed()
\r
1164 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1171 * @param e DOCUMENT ME!
\r
1173 public void showText_actionPerformed()
\r
1175 getGroup().setDisplayText(showText.isSelected());
\r
1182 * @param e DOCUMENT ME!
\r
1184 public void showColourText_actionPerformed()
\r
1186 getGroup().setColourText(showColourText.isSelected());
\r
1190 public void showLink(String url)
\r
1194 jalview.util.BrowserLauncher.openURL(url);
\r
1196 catch (Exception ex)
\r
1198 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1199 "Unixers: Couldn't find default web browser."
\r
1201 "\nAdd the full path to your browser in Preferences.",
\r
1202 "Web browser not found",
\r
1203 JOptionPane.WARNING_MESSAGE);
\r
1205 ex.printStackTrace();
\r
1209 void hideSequences(boolean representGroup)
\r
1211 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1212 if (sg == null || sg.getSize() < 1)
\r
1214 ap.av.hideSequence(new SequenceI[]
\r
1219 ap.av.setSelectionGroup(null);
\r
1221 if (representGroup)
\r
1223 ap.av.hideRepSequences(sequence, sg);
\r
1228 int gsize = sg.getSize();
\r
1229 SequenceI[] hseqs;
\r
1231 hseqs = new SequenceI[gsize];
\r
1234 for (int i = 0; i < gsize; i++)
\r
1236 hseqs[index++] = sg.getSequenceAt(i);
\r
1239 ap.av.hideSequence(hseqs);
\r
1242 public void copy_actionPerformed()
\r
1244 ap.alignFrame.copy_actionPerformed(null);
\r
1247 public void cut_actionPerformed()
\r
1249 ap.alignFrame.cut_actionPerformed(null);
\r
1252 void changeCase(ActionEvent e)
\r
1254 Object source = e.getSource();
\r
1255 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1259 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
\r
1260 sg.getStartRes(), sg.getEndRes() + 1);
\r
1262 String description;
\r
1265 if (source == toggle)
\r
1267 description = "Toggle Case";
\r
1268 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1270 else if (source == upperCase)
\r
1272 description = "To Upper Case";
\r
1273 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1277 description = "To Lower Case";
\r
1278 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1281 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1282 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1283 startEnd, caseChange
\r
1286 ap.alignFrame.addHistoryItem(caseCommand);
\r
1288 ap.av.firePropertyChange("alignment", null,
\r
1289 ap.av.getAlignment().getSequences());
\r
1294 public void outputText_actionPerformed(ActionEvent e)
\r
1296 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1297 cap.setForInput(null);
\r
1298 Desktop.addInternalFrame(cap,
\r
1299 "Alignment output - " + e.getActionCommand(), 600,
\r
1302 String[] omitHidden = null;
\r
1304 if (ap.av.hasHiddenColumns)
\r
1306 System.out.println("PROMPT USER HERE");
\r
1307 omitHidden = ap.av.getViewAsString(true);
\r
1310 cap.setText(new FormatAdapter().formatSequences(
\r
1311 e.getActionCommand(),
\r
1312 ap.av.getSelectionAsNewSequence(),
\r
1316 public void pdbFromFile_actionPerformed()
\r
1318 jalview.io.JalviewFileChooser chooser
\r
1319 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1321 "LAST_DIRECTORY"));
\r
1322 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1323 chooser.setDialogTitle("Select a PDB file");
\r
1324 chooser.setToolTipText("Load a PDB file");
\r
1326 int value = chooser.showOpenDialog(null);
\r
1328 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1330 PDBEntry entry = new PDBEntry();
\r
1331 String choice = chooser.getSelectedFile().getPath();
\r
1332 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1335 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1336 jalview.io.AppletFormatAdapter.FILE);
\r
1338 if (pdbfile.id == null)
\r
1340 String reply = JOptionPane.showInternalInputDialog(
\r
1342 "Couldn't find a PDB id in the file supplied."
\r
1343 + "Please enter an Id to identify this structure.",
\r
1344 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1345 if (reply == null)
\r
1350 entry.setId(reply);
\r
1354 entry.setId(pdbfile.id);
\r
1357 catch (java.io.IOException ex)
\r
1359 ex.printStackTrace();
\r
1362 entry.setFile(choice);
\r
1363 sequence.getDatasetSequence().addPDBId(entry);
\r
1368 public void enterPDB_actionPerformed()
\r
1370 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1371 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1373 if (id != null && id.length() > 0)
\r
1375 PDBEntry entry = new PDBEntry();
\r
1377 sequence.getDatasetSequence()
\r
1382 public void discoverPDB_actionPerformed()
\r
1384 SequenceI[] sequences =
\r
1385 ap.av.selectionGroup == null ?
\r
1386 new Sequence[]{sequence}
\r
1387 : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
\r
1389 new jalview.io.DBRefFetcher(sequences,
\r
1390 ap.alignFrame).fetchDBRefs(false);
\r
1393 public void sequenceFeature_actionPerformed()
\r
1395 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1401 int gSize = sg.getSize();
\r
1402 SequenceI[] seqs = new SequenceI[gSize];
\r
1403 SequenceFeature[] features = new SequenceFeature[gSize];
\r
1405 for (int i = 0; i < gSize; i++)
\r
1407 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1408 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1409 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1410 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
\r
1413 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1414 .amendFeatures(seqs, features, true, ap))
\r
1416 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1417 ap.av.setShowSequenceFeatures(true);
\r
1418 ap.highlightSearchResults(null);
\r
1422 public void textColour_actionPerformed()
\r
1424 SequenceGroup sg = getGroup();
\r
1427 new TextColourChooser().chooseColour(ap, sg);
\r
1431 public void colourByStructure(String pdbid)
\r
1433 Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
\r
1434 .colourSequenceFromStructure(sequence, pdbid);
\r
1436 AlignmentAnnotation an = new AlignmentAnnotation(
\r
1437 "Structure", "Coloured by "+pdbid, anots);
\r
1439 ap.av.alignment.addAnnotation(an);
\r
1440 an.createSequenceMapping(sequence, 0, true);
\r
1441 //an.adjustForAlignment();
\r
1442 ap.av.alignment.setAnnotationIndex(an,0);
\r
1444 ap.adjustAnnotationHeight();
\r
1446 sequence.addAlignmentAnnotation(an);
\r
1450 public void editSequence_actionPerformed(ActionEvent actionEvent)
\r
1452 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1456 if (sequence == null)
\r
1457 sequence = (Sequence) sg.getSequenceAt(0);
\r
1459 EditNameDialog dialog = new EditNameDialog(
\r
1460 sequence.getSequenceAsString(
\r
1462 sg.getEndRes() + 1),
\r
1468 if (dialog.accept)
\r
1470 EditCommand editCommand = new EditCommand(
\r
1471 "Edit Sequences", EditCommand.REPLACE,
\r
1472 dialog.getName().replace(' ', ap.av.getGapCharacter()),
\r
1473 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1474 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
\r
1477 ap.alignFrame.addHistoryItem(editCommand);
\r
1479 ap.av.firePropertyChange("alignment", null,
\r
1480 ap.av.getAlignment().getSequences());
\r