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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155 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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158 while (e.hasMoreElements())
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160 final PDBEntry pdb = (PDBEntry) e.nextElement();
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162 menuItem = new JMenuItem();
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163 menuItem.setText(pdb.getId());
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164 menuItem.addActionListener(new java.awt.event.ActionListener()
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166 public void actionPerformed(ActionEvent e)
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168 Vector seqs = new Vector();
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169 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
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171 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
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175 for(int p=0; p<pdbs.size(); p++)
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177 PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
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178 if(p1.getId().equals(pdb.getId()))
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180 if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
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181 seqs.addElement(ap.av.alignment.getSequenceAt(i));
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188 SequenceI [] seqs2 = new SequenceI[seqs.size()];
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189 seqs.toArray(seqs2);
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191 new AppJMol(pdb, seqs2, ap);
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194 viewStructureMenu.add(menuItem);
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196 /* menuItem = new JMenuItem();
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197 menuItem.setText(pdb.getId());
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198 menuItem.addActionListener(new java.awt.event.ActionListener()
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200 public void actionPerformed(ActionEvent e)
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202 colourByStructure(pdb.getId());
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205 colStructureMenu.add(menuItem);*/
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210 structureMenu.remove(viewStructureMenu);
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211 // structureMenu.remove(colStructureMenu);
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214 menuItem = new JMenuItem("Hide Sequences");
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215 menuItem.addActionListener(new java.awt.event.ActionListener()
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217 public void actionPerformed(ActionEvent e)
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219 hideSequences(false);
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224 if (ap.av.getSelectionGroup() != null
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225 && ap.av.getSelectionGroup().getSize() > 1)
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227 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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228 menuItem.addActionListener(new java.awt.event.ActionListener()
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230 public void actionPerformed(ActionEvent e)
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232 hideSequences(true);
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235 sequenceMenu.add(menuItem);
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238 if (ap.av.hasHiddenRows)
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240 final int index = ap.av.alignment.findIndex(seq);
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242 if (ap.av.adjustForHiddenSeqs(index) -
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243 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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245 menuItem = new JMenuItem("Reveal Sequences");
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246 menuItem.addActionListener(new ActionListener()
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248 public void actionPerformed(ActionEvent e)
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250 ap.av.showSequence(index);
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251 if (ap.overviewPanel != null)
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253 ap.overviewPanel.updateOverviewImage();
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260 menuItem = new JMenuItem("Reveal All");
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261 menuItem.addActionListener(new ActionListener()
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263 public void actionPerformed(ActionEvent e)
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265 ap.av.showAllHiddenSeqs();
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266 if (ap.overviewPanel != null)
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268 ap.overviewPanel.updateOverviewImage();
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278 SequenceGroup sg = ap.av.getSelectionGroup();
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282 groupName.setText(sg.getName());
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284 if (sg.cs instanceof ZappoColourScheme)
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286 zappoColour.setSelected(true);
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288 else if (sg.cs instanceof TaylorColourScheme)
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290 taylorColour.setSelected(true);
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292 else if (sg.cs instanceof PIDColourScheme)
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294 PIDColour.setSelected(true);
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296 else if (sg.cs instanceof Blosum62ColourScheme)
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298 BLOSUM62Colour.setSelected(true);
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300 else if (sg.cs instanceof UserColourScheme)
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302 userDefinedColour.setSelected(true);
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304 else if (sg.cs instanceof HydrophobicColourScheme)
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306 hydrophobicityColour.setSelected(true);
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308 else if (sg.cs instanceof HelixColourScheme)
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310 helixColour.setSelected(true);
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312 else if (sg.cs instanceof StrandColourScheme)
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314 strandColour.setSelected(true);
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316 else if (sg.cs instanceof TurnColourScheme)
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318 turnColour.setSelected(true);
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320 else if (sg.cs instanceof BuriedColourScheme)
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322 buriedColour.setSelected(true);
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324 else if (sg.cs instanceof ClustalxColourScheme)
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326 clustalColour.setSelected(true);
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330 noColourmenuItem.setSelected(true);
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333 if (sg.cs != null && sg.cs.conservationApplied())
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335 conservationMenuItem.setSelected(true);
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338 showText.setSelected(sg.getDisplayText());
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339 showColourText.setSelected(sg.getColourText());
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340 showBoxes.setSelected(sg.getDisplayBoxes());
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344 groupMenu.setVisible(false);
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345 editMenu.setVisible(false);
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348 if (!ap.av.alignment.getGroups().contains(sg))
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350 unGroupMenuItem.setVisible(false);
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355 sequenceMenu.setVisible(false);
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356 structureMenu.setVisible(false);
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359 if (links != null && links.size() > 0)
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361 JMenu linkMenu = new JMenu("Link");
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363 for (int i = 0; i < links.size(); i++)
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365 String link = links.elementAt(i).toString();
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366 final String label = link.substring(0, link.indexOf("|"));
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367 item = new JMenuItem(label);
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370 if (link.indexOf("$SEQUENCE_ID$") > -1)
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372 String id = seq.getName();
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373 if (id.indexOf("|") > -1)
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375 id = id.substring(id.lastIndexOf("|") + 1);
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378 url = link.substring(link.indexOf("|") + 1,
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379 link.indexOf("$SEQUENCE_ID$"))
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381 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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385 url = link.substring(link.lastIndexOf("|") + 1);
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388 item.addActionListener(new java.awt.event.ActionListener()
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390 public void actionPerformed(ActionEvent e)
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396 linkMenu.add(item);
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398 if (sequence != null)
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400 sequenceMenu.add(linkMenu);
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412 * @throws Exception DOCUMENT ME!
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414 private void jbInit()
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417 groupMenu.setText("Group");
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418 groupMenu.setText("Selection");
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419 groupName.setText("Name");
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420 groupName.addActionListener(new java.awt.event.ActionListener()
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422 public void actionPerformed(ActionEvent e)
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424 groupName_actionPerformed();
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427 sequenceMenu.setText("Sequence");
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428 sequenceName.setText("Edit Name/Description");
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429 sequenceName.addActionListener(new java.awt.event.ActionListener()
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431 public void actionPerformed(ActionEvent e)
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433 sequenceName_actionPerformed();
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436 PIDColour.setFocusPainted(false);
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437 unGroupMenuItem.setText("Remove Group");
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438 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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440 public void actionPerformed(ActionEvent e)
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442 unGroupMenuItem_actionPerformed();
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446 outline.setText("Border colour");
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447 outline.addActionListener(new java.awt.event.ActionListener()
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449 public void actionPerformed(ActionEvent e)
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451 outline_actionPerformed();
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454 nucleotideMenuItem.setText("Nucleotide");
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455 nucleotideMenuItem.addActionListener(new ActionListener()
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457 public void actionPerformed(ActionEvent e)
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459 nucleotideMenuItem_actionPerformed();
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462 colourMenu.setText("Group Colour");
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463 showBoxes.setText("Boxes");
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464 showBoxes.setState(true);
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465 showBoxes.addActionListener(new ActionListener()
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467 public void actionPerformed(ActionEvent e)
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469 showBoxes_actionPerformed();
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472 showText.setText("Text");
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473 showText.setState(true);
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474 showText.addActionListener(new ActionListener()
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476 public void actionPerformed(ActionEvent e)
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478 showText_actionPerformed();
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481 showColourText.setText("Colour Text");
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482 showColourText.addActionListener(new ActionListener()
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484 public void actionPerformed(ActionEvent e)
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486 showColourText_actionPerformed();
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489 editMenu.setText("Edit");
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490 cut.setText("Cut");
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491 cut.addActionListener(new ActionListener()
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493 public void actionPerformed(ActionEvent e)
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495 cut_actionPerformed();
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498 upperCase.setText("To Upper Case");
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499 upperCase.addActionListener(new ActionListener()
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501 public void actionPerformed(ActionEvent e)
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506 copy.setText("Copy");
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507 copy.addActionListener(new ActionListener()
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509 public void actionPerformed(ActionEvent e)
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511 copy_actionPerformed();
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514 lowerCase.setText("To Lower Case");
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515 lowerCase.addActionListener(new ActionListener()
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517 public void actionPerformed(ActionEvent e)
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522 toggle.setText("Toggle Case");
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523 toggle.addActionListener(new ActionListener()
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525 public void actionPerformed(ActionEvent e)
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530 pdbMenu.setText("Associate Structure with Sequence");
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531 pdbFromFile.setText("From File");
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532 pdbFromFile.addActionListener(new ActionListener()
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534 public void actionPerformed(ActionEvent e)
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536 pdbFromFile_actionPerformed();
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539 enterPDB.setText("Enter PDB Id");
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540 enterPDB.addActionListener(new ActionListener()
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542 public void actionPerformed(ActionEvent e)
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544 enterPDB_actionPerformed();
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547 discoverPDB.setText("Discover PDB ids");
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548 discoverPDB.addActionListener(new ActionListener()
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550 public void actionPerformed(ActionEvent e)
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552 discoverPDB_actionPerformed();
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555 outputMenu.setText("Output to Textbox...");
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556 sequenceFeature.setText("Create Sequence Feature");
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557 sequenceFeature.addActionListener(new ActionListener()
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559 public void actionPerformed(ActionEvent e)
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561 sequenceFeature_actionPerformed();
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564 textColour.setText("Text Colour");
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565 textColour.addActionListener(new ActionListener()
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567 public void actionPerformed(ActionEvent e)
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569 textColour_actionPerformed();
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572 jMenu1.setText("Group");
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573 structureMenu.setText("Structure");
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574 viewStructureMenu.setText("View Structure");
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575 // colStructureMenu.setText("Colour By Structure");
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576 editSequence.setText("Edit Sequence...");
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577 editSequence.addActionListener(new ActionListener()
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579 public void actionPerformed(ActionEvent actionEvent)
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581 editSequence_actionPerformed(actionEvent);
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584 /* annotationMenuItem.setText("By Annotation");
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585 annotationMenuItem.addActionListener(new ActionListener()
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587 public void actionPerformed(ActionEvent actionEvent)
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589 annotationMenuItem_actionPerformed(actionEvent);
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596 this.add(structureMenu);
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597 groupMenu.add(editMenu);
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598 groupMenu.add(outputMenu);
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599 groupMenu.add(sequenceFeature);
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600 groupMenu.add(jMenu1);
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601 sequenceMenu.add(sequenceName);
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602 colourMenu.add(textColour);
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603 colourMenu.add(noColourmenuItem);
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604 colourMenu.add(clustalColour);
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605 colourMenu.add(BLOSUM62Colour);
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606 colourMenu.add(PIDColour);
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607 colourMenu.add(zappoColour);
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608 colourMenu.add(taylorColour);
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609 colourMenu.add(hydrophobicityColour);
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610 colourMenu.add(helixColour);
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611 colourMenu.add(strandColour);
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612 colourMenu.add(turnColour);
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613 colourMenu.add(buriedColour);
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614 colourMenu.add(nucleotideMenuItem);
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615 colourMenu.add(userDefinedColour);
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617 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
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619 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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620 getUserColourSchemes().keys();
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622 while (userColours.hasMoreElements())
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624 JMenuItem item = new JMenuItem(userColours.
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625 nextElement().toString());
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626 item.addActionListener(new ActionListener()
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628 public void actionPerformed(ActionEvent evt)
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630 userDefinedColour_actionPerformed(evt);
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633 colourMenu.add(item);
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637 colourMenu.addSeparator();
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638 colourMenu.add(abovePIDColour);
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639 colourMenu.add(conservationMenuItem);
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640 //colourMenu.add(annotationMenuItem);
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641 editMenu.add(copy);
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643 editMenu.add(editSequence);
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644 editMenu.add(upperCase);
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645 editMenu.add(lowerCase);
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646 editMenu.add(toggle);
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647 pdbMenu.add(pdbFromFile);
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648 pdbMenu.add(enterPDB);
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649 pdbMenu.add(discoverPDB);
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650 jMenu1.add(groupName);
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651 jMenu1.add(unGroupMenuItem);
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652 jMenu1.add(colourMenu);
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653 jMenu1.add(showBoxes);
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654 jMenu1.add(showText);
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655 jMenu1.add(showColourText);
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656 jMenu1.add(outline);
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657 structureMenu.add(pdbMenu);
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658 structureMenu.add(viewStructureMenu);
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659 // structureMenu.add(colStructureMenu);
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660 noColourmenuItem.setText("None");
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661 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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663 public void actionPerformed(ActionEvent e)
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665 noColourmenuItem_actionPerformed();
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669 clustalColour.setText("Clustalx colours");
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670 clustalColour.addActionListener(new java.awt.event.ActionListener()
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672 public void actionPerformed(ActionEvent e)
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674 clustalColour_actionPerformed();
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677 zappoColour.setText("Zappo");
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678 zappoColour.addActionListener(new java.awt.event.ActionListener()
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680 public void actionPerformed(ActionEvent e)
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682 zappoColour_actionPerformed();
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685 taylorColour.setText("Taylor");
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686 taylorColour.addActionListener(new java.awt.event.ActionListener()
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688 public void actionPerformed(ActionEvent e)
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690 taylorColour_actionPerformed();
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693 hydrophobicityColour.setText("Hydrophobicity");
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694 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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696 public void actionPerformed(ActionEvent e)
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698 hydrophobicityColour_actionPerformed();
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701 helixColour.setText("Helix propensity");
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702 helixColour.addActionListener(new java.awt.event.ActionListener()
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704 public void actionPerformed(ActionEvent e)
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706 helixColour_actionPerformed();
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709 strandColour.setText("Strand propensity");
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710 strandColour.addActionListener(new java.awt.event.ActionListener()
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712 public void actionPerformed(ActionEvent e)
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714 strandColour_actionPerformed();
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717 turnColour.setText("Turn propensity");
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718 turnColour.addActionListener(new java.awt.event.ActionListener()
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720 public void actionPerformed(ActionEvent e)
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722 turnColour_actionPerformed();
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725 buriedColour.setText("Buried Index");
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726 buriedColour.addActionListener(new java.awt.event.ActionListener()
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728 public void actionPerformed(ActionEvent e)
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730 buriedColour_actionPerformed();
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733 abovePIDColour.setText("Above % Identity");
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734 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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736 public void actionPerformed(ActionEvent e)
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738 abovePIDColour_actionPerformed();
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741 userDefinedColour.setText("User Defined...");
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742 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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744 public void actionPerformed(ActionEvent e)
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746 userDefinedColour_actionPerformed(e);
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749 PIDColour.setText("Percentage Identity");
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750 PIDColour.addActionListener(new java.awt.event.ActionListener()
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752 public void actionPerformed(ActionEvent e)
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754 PIDColour_actionPerformed();
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757 BLOSUM62Colour.setText("BLOSUM62");
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758 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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760 public void actionPerformed(ActionEvent e)
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762 BLOSUM62Colour_actionPerformed();
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765 conservationMenuItem.setText("Conservation");
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766 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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768 public void actionPerformed(ActionEvent e)
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770 conservationMenuItem_actionPerformed();
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780 ap.paintAlignment(true);
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782 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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788 * @param e DOCUMENT ME!
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790 protected void clustalColour_actionPerformed()
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792 SequenceGroup sg = getGroup();
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793 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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794 ap.av.alignment.getWidth());
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801 * @param e DOCUMENT ME!
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803 protected void zappoColour_actionPerformed()
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805 getGroup().cs = new ZappoColourScheme();
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812 * @param e DOCUMENT ME!
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814 protected void taylorColour_actionPerformed()
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816 getGroup().cs = new TaylorColourScheme();
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823 * @param e DOCUMENT ME!
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825 protected void hydrophobicityColour_actionPerformed()
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827 getGroup().cs = new HydrophobicColourScheme();
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834 * @param e DOCUMENT ME!
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836 protected void helixColour_actionPerformed()
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838 getGroup().cs = new HelixColourScheme();
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845 * @param e DOCUMENT ME!
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847 protected void strandColour_actionPerformed()
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849 getGroup().cs = new StrandColourScheme();
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856 * @param e DOCUMENT ME!
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858 protected void turnColour_actionPerformed()
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860 getGroup().cs = new TurnColourScheme();
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867 * @param e DOCUMENT ME!
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869 protected void buriedColour_actionPerformed()
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871 getGroup().cs = new BuriedColourScheme();
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878 * @param e DOCUMENT ME!
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880 public void nucleotideMenuItem_actionPerformed()
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882 getGroup().cs = new NucleotideColourScheme();
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889 * @param e DOCUMENT ME!
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891 protected void abovePIDColour_actionPerformed()
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893 SequenceGroup sg = getGroup();
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899 if (abovePIDColour.isSelected())
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901 sg.cs.setConsensus(AAFrequency.calculate(
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902 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
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903 sg.getEndRes() + 1));
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905 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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906 getGroup().getName());
\r
908 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
\r
910 SliderPanel.showPIDSlider();
\r
912 else // remove PIDColouring
\r
914 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
923 * @param e DOCUMENT ME!
\r
925 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
927 SequenceGroup sg = getGroup();
\r
929 if (e.getActionCommand().equals("User Defined..."))
\r
931 new UserDefinedColours(ap, sg);
\r
935 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
936 getUserColourSchemes().get(e.getActionCommand());
\r
946 * @param e DOCUMENT ME!
\r
948 protected void PIDColour_actionPerformed()
\r
950 SequenceGroup sg = getGroup();
\r
951 sg.cs = new PIDColourScheme();
\r
952 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
953 hiddenRepSequences),
\r
955 sg.getEndRes() + 1));
\r
962 * @param e DOCUMENT ME!
\r
964 protected void BLOSUM62Colour_actionPerformed()
\r
966 SequenceGroup sg = getGroup();
\r
968 sg.cs = new Blosum62ColourScheme();
\r
970 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
971 hiddenRepSequences),
\r
973 sg.getEndRes() + 1));
\r
981 * @param e DOCUMENT ME!
\r
983 protected void noColourmenuItem_actionPerformed()
\r
985 getGroup().cs = null;
\r
992 * @param e DOCUMENT ME!
\r
994 protected void conservationMenuItem_actionPerformed()
\r
996 SequenceGroup sg = getGroup();
\r
1002 if (conservationMenuItem.isSelected())
\r
1004 Conservation c = new Conservation("Group",
\r
1005 ResidueProperties.propHash, 3,
\r
1006 sg.getSequences(ap.av.
\r
1007 hiddenRepSequences),
\r
1009 sg.getEndRes() + 1);
\r
1012 c.verdict(false, ap.av.ConsPercGaps);
\r
1014 sg.cs.setConservation(c);
\r
1016 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
1017 SliderPanel.showConservationSlider();
\r
1019 else // remove ConservationColouring
\r
1021 sg.cs.setConservation(null);
\r
1027 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
\r
1029 SequenceGroup sg = getGroup();
\r
1035 AnnotationColourGradient acg = new AnnotationColourGradient(
\r
1036 sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
\r
1038 acg.predefinedColours = true;
\r
1047 * @param e DOCUMENT ME!
\r
1049 protected void groupName_actionPerformed()
\r
1052 SequenceGroup sg = getGroup();
\r
1053 EditNameDialog dialog = new EditNameDialog(sg.getName(),
\r
1054 sg.getDescription(),
\r
1056 "Group Description ",
\r
1057 "Edit Group Name/Description");
\r
1059 if (!dialog.accept)
\r
1064 sg.setName(dialog.getName());
\r
1065 sg.setDescription(dialog.getDescription());
\r
1071 * @return DOCUMENT ME!
\r
1073 SequenceGroup getGroup()
\r
1075 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1076 // this method won't add a new group if it already exists
\r
1079 ap.av.alignment.addGroup(sg);
\r
1088 * @param e DOCUMENT ME!
\r
1090 void sequenceName_actionPerformed()
\r
1092 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
\r
1093 sequence.getDescription(),
\r
1094 " Sequence Name ",
\r
1095 "Sequence Description ",
\r
1096 "Edit Sequence Name/Description");
\r
1098 if (!dialog.accept)
\r
1103 if (dialog.getName() != null)
\r
1105 if (dialog.getName().indexOf(" ") > -1)
\r
1107 JOptionPane.showMessageDialog(ap,
\r
1108 "Spaces have been converted to \"_\"",
\r
1109 "No spaces allowed in Sequence Name",
\r
1110 JOptionPane.WARNING_MESSAGE);
\r
1113 sequence.setName(dialog.getName().replace(' ', '_'));
\r
1114 ap.paintAlignment(false);
\r
1117 sequence.setDescription(dialog.getDescription());
\r
1119 ap.av.firePropertyChange("alignment", null,
\r
1120 ap.av.getAlignment().getSequences());
\r
1127 * @param e DOCUMENT ME!
\r
1129 void unGroupMenuItem_actionPerformed()
\r
1131 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1132 ap.av.alignment.deleteGroup(sg);
\r
1133 ap.av.setSelectionGroup(null);
\r
1140 * @param e DOCUMENT ME!
\r
1142 protected void outline_actionPerformed()
\r
1144 SequenceGroup sg = getGroup();
\r
1145 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1150 sg.setOutlineColour(col);
\r
1159 * @param e DOCUMENT ME!
\r
1161 public void showBoxes_actionPerformed()
\r
1163 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1170 * @param e DOCUMENT ME!
\r
1172 public void showText_actionPerformed()
\r
1174 getGroup().setDisplayText(showText.isSelected());
\r
1181 * @param e DOCUMENT ME!
\r
1183 public void showColourText_actionPerformed()
\r
1185 getGroup().setColourText(showColourText.isSelected());
\r
1189 public void showLink(String url)
\r
1193 jalview.util.BrowserLauncher.openURL(url);
\r
1195 catch (Exception ex)
\r
1197 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1198 "Unixers: Couldn't find default web browser."
\r
1200 "\nAdd the full path to your browser in Preferences.",
\r
1201 "Web browser not found",
\r
1202 JOptionPane.WARNING_MESSAGE);
\r
1204 ex.printStackTrace();
\r
1208 void hideSequences(boolean representGroup)
\r
1210 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1211 if (sg == null || sg.getSize() < 1)
\r
1213 ap.av.hideSequence(new SequenceI[]
\r
1218 ap.av.setSelectionGroup(null);
\r
1220 if (representGroup)
\r
1222 ap.av.hideRepSequences(sequence, sg);
\r
1227 int gsize = sg.getSize();
\r
1228 SequenceI[] hseqs;
\r
1230 hseqs = new SequenceI[gsize];
\r
1233 for (int i = 0; i < gsize; i++)
\r
1235 hseqs[index++] = sg.getSequenceAt(i);
\r
1238 ap.av.hideSequence(hseqs);
\r
1241 public void copy_actionPerformed()
\r
1243 ap.alignFrame.copy_actionPerformed(null);
\r
1246 public void cut_actionPerformed()
\r
1248 ap.alignFrame.cut_actionPerformed(null);
\r
1251 void changeCase(ActionEvent e)
\r
1253 Object source = e.getSource();
\r
1254 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1258 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
\r
1259 sg.getStartRes(), sg.getEndRes() + 1);
\r
1261 String description;
\r
1264 if (source == toggle)
\r
1266 description = "Toggle Case";
\r
1267 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1269 else if (source == upperCase)
\r
1271 description = "To Upper Case";
\r
1272 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1276 description = "To Lower Case";
\r
1277 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1280 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1281 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1282 startEnd, caseChange
\r
1285 ap.alignFrame.addHistoryItem(caseCommand);
\r
1287 ap.av.firePropertyChange("alignment", null,
\r
1288 ap.av.getAlignment().getSequences());
\r
1293 public void outputText_actionPerformed(ActionEvent e)
\r
1295 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1296 cap.setForInput(null);
\r
1297 Desktop.addInternalFrame(cap,
\r
1298 "Alignment output - " + e.getActionCommand(), 600,
\r
1301 String[] omitHidden = null;
\r
1303 if (ap.av.hasHiddenColumns)
\r
1305 System.out.println("PROMPT USER HERE");
\r
1306 omitHidden = ap.av.getViewAsString(true);
\r
1309 cap.setText(new FormatAdapter().formatSequences(
\r
1310 e.getActionCommand(),
\r
1311 ap.av.getSelectionAsNewSequence(),
\r
1315 public void pdbFromFile_actionPerformed()
\r
1317 jalview.io.JalviewFileChooser chooser
\r
1318 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1320 "LAST_DIRECTORY"));
\r
1321 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1322 chooser.setDialogTitle("Select a PDB file");
\r
1323 chooser.setToolTipText("Load a PDB file");
\r
1325 int value = chooser.showOpenDialog(null);
\r
1327 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1329 PDBEntry entry = new PDBEntry();
\r
1330 String choice = chooser.getSelectedFile().getPath();
\r
1331 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1334 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1335 jalview.io.AppletFormatAdapter.FILE);
\r
1337 if (pdbfile.id == null)
\r
1339 String reply = JOptionPane.showInternalInputDialog(
\r
1341 "Couldn't find a PDB id in the file supplied."
\r
1342 + "Please enter an Id to identify this structure.",
\r
1343 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1344 if (reply == null)
\r
1349 entry.setId(reply);
\r
1353 entry.setId(pdbfile.id);
\r
1356 catch (java.io.IOException ex)
\r
1358 ex.printStackTrace();
\r
1361 entry.setFile(choice);
\r
1362 sequence.getDatasetSequence().addPDBId(entry);
\r
1367 public void enterPDB_actionPerformed()
\r
1369 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1370 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1372 if (id != null && id.length() > 0)
\r
1374 PDBEntry entry = new PDBEntry();
\r
1376 sequence.getDatasetSequence()
\r
1381 public void discoverPDB_actionPerformed()
\r
1383 SequenceI[] sequences =
\r
1384 ap.av.selectionGroup == null ?
\r
1385 new Sequence[]{sequence}
\r
1386 : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
\r
1388 new jalview.io.DBRefFetcher(sequences,
\r
1389 ap.alignFrame).fetchDBRefs(false);
\r
1392 public void sequenceFeature_actionPerformed()
\r
1394 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1400 int gSize = sg.getSize();
\r
1401 SequenceI[] seqs = new SequenceI[gSize];
\r
1402 SequenceFeature[] features = new SequenceFeature[gSize];
\r
1404 for (int i = 0; i < gSize; i++)
\r
1406 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1407 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1408 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1409 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
\r
1412 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1413 .amendFeatures(seqs, features, true, ap))
\r
1415 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1416 ap.av.setShowSequenceFeatures(true);
\r
1417 ap.highlightSearchResults(null);
\r
1421 public void textColour_actionPerformed()
\r
1423 SequenceGroup sg = getGroup();
\r
1426 new TextColourChooser().chooseColour(ap, sg);
\r
1430 public void colourByStructure(String pdbid)
\r
1432 Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
\r
1433 .colourSequenceFromStructure(sequence, pdbid);
\r
1435 AlignmentAnnotation an = new AlignmentAnnotation(
\r
1436 "Structure", "Coloured by "+pdbid, anots);
\r
1438 ap.av.alignment.addAnnotation(an);
\r
1439 an.createSequenceMapping(sequence, 0, true);
\r
1440 //an.adjustForAlignment();
\r
1441 ap.av.alignment.setAnnotationIndex(an,0);
\r
1443 ap.adjustAnnotationHeight();
\r
1445 sequence.addAlignmentAnnotation(an);
\r
1449 public void editSequence_actionPerformed(ActionEvent actionEvent)
\r
1451 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1455 if (sequence == null)
\r
1456 sequence = (Sequence) sg.getSequenceAt(0);
\r
1458 EditNameDialog dialog = new EditNameDialog(
\r
1459 sequence.getSequenceAsString(
\r
1461 sg.getEndRes() + 1),
\r
1467 if (dialog.accept)
\r
1469 EditCommand editCommand = new EditCommand(
\r
1470 "Edit Sequences", EditCommand.REPLACE,
\r
1472 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1473 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
\r
1476 ap.alignFrame.addHistoryItem(editCommand);
\r
1478 ap.av.firePropertyChange("alignment", null,
\r
1479 ap.av.getAlignment().getSequences());
\r