2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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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23 import jalview.analysis.*;
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24 import jalview.datamodel.*;
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25 import jalview.schemes.*;
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26 import jalview.commands.ChangeCaseCommand;
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29 import java.awt.event.*;
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31 import javax.swing.*;
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33 import java.util.Vector;
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34 import jalview.io.FormatAdapter;
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41 * @version $Revision$
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43 public class PopupMenu extends JPopupMenu
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45 JMenu groupMenu = new JMenu();
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46 JMenuItem groupName = new JMenuItem();
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47 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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48 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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49 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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55 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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56 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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58 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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59 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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60 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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62 JMenu sequenceMenu = new JMenu();
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63 JMenuItem sequenceName = new JMenuItem();
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65 JMenuItem unGroupMenuItem = new JMenuItem();
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66 JMenuItem outline = new JMenuItem();
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67 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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68 JMenu colourMenu = new JMenu();
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69 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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70 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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71 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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72 JMenu editMenu = new JMenu();
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73 JMenuItem cut = new JMenuItem();
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74 JMenuItem copy = new JMenuItem();
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75 JMenuItem upperCase = new JMenuItem();
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76 JMenuItem lowerCase = new JMenuItem();
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77 JMenuItem toggle = new JMenuItem();
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78 JMenu pdbMenu = new JMenu();
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79 JMenuItem pdbFromFile = new JMenuItem();
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80 JMenuItem enterPDB = new JMenuItem();
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81 JMenuItem discoverPDB = new JMenuItem();
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82 JMenu outputMenu = new JMenu();
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83 JMenuItem sequenceFeature = new JMenuItem();
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86 * Creates a new PopupMenu object.
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88 * @param ap DOCUMENT ME!
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89 * @param seq DOCUMENT ME!
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91 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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93 ///////////////////////////////////////////////////////////
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94 // If this is activated from the sequence panel, the user may want to
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95 // edit or annotate a particular residue. Therefore display the residue menu
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97 // If from the IDPanel, we must display the sequence menu
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98 //////////////////////////////////////////////////////////
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102 ButtonGroup colours = new ButtonGroup();
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103 colours.add(noColourmenuItem);
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104 colours.add(clustalColour);
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105 colours.add(zappoColour);
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106 colours.add(taylorColour);
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107 colours.add(hydrophobicityColour);
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108 colours.add(helixColour);
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109 colours.add(strandColour);
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110 colours.add(turnColour);
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111 colours.add(buriedColour);
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112 colours.add(abovePIDColour);
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113 colours.add(userDefinedColour);
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114 colours.add(PIDColour);
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115 colours.add(BLOSUM62Colour);
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117 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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119 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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121 item.addActionListener(new java.awt.event.ActionListener()
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123 public void actionPerformed(ActionEvent e)
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125 outputText_actionPerformed(e);
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129 outputMenu.add(item);
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137 catch (Exception e)
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139 e.printStackTrace();
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145 int start = Math.max(sequence.getName().length()-15, 0);
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146 sequenceMenu.setText(sequence.getName().substring(start));
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148 JMenuItem menuItem;
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149 if( seq.getDatasetSequence().getPDBId() != null)
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151 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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154 while (e.hasMoreElements())
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156 final PDBEntry pdb = (PDBEntry) e.nextElement();
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158 menuItem = new JMenuItem();
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159 menuItem.setText("View PDB entry: " + pdb.getId());
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160 menuItem.addActionListener(new java.awt.event.ActionListener()
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162 public void actionPerformed(ActionEvent e)
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164 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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167 sequenceMenu.add(menuItem);
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171 menuItem = new JMenuItem("Hide Sequences");
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172 menuItem.addActionListener(new java.awt.event.ActionListener()
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174 public void actionPerformed(ActionEvent e)
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176 hideSequences(false);
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181 if(ap.av.getSelectionGroup() !=null
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182 && ap.av.getSelectionGroup().getSize(false)>1)
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184 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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185 menuItem.addActionListener(new java.awt.event.ActionListener()
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187 public void actionPerformed(ActionEvent e)
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189 hideSequences(true);
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192 sequenceMenu.add(menuItem);
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195 if (ap.av.hasHiddenRows)
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197 final int index = ap.av.alignment.findIndex(seq);
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199 if (ap.av.adjustForHiddenSeqs(index) -
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200 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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202 menuItem = new JMenuItem("Reveal Sequences");
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203 menuItem.addActionListener(new ActionListener()
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205 public void actionPerformed(ActionEvent e)
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207 ap.av.showSequence(index);
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208 if (ap.overviewPanel != null)
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209 ap.overviewPanel.updateOverviewImage();
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215 menuItem = new JMenuItem("Reveal All");
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216 menuItem.addActionListener(new ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 ap.av.showAllHiddenSeqs();
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221 if (ap.overviewPanel != null)
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222 ap.overviewPanel.updateOverviewImage();
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234 SequenceGroup sg = ap.av.getSelectionGroup();
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238 groupName.setText(sg.getName());
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240 if (sg.cs instanceof ZappoColourScheme)
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242 zappoColour.setSelected(true);
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244 else if (sg.cs instanceof TaylorColourScheme)
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246 taylorColour.setSelected(true);
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248 else if (sg.cs instanceof PIDColourScheme)
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250 PIDColour.setSelected(true);
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252 else if (sg.cs instanceof Blosum62ColourScheme)
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254 BLOSUM62Colour.setSelected(true);
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256 else if (sg.cs instanceof UserColourScheme)
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258 userDefinedColour.setSelected(true);
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260 else if (sg.cs instanceof HydrophobicColourScheme)
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262 hydrophobicityColour.setSelected(true);
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264 else if (sg.cs instanceof HelixColourScheme)
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266 helixColour.setSelected(true);
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268 else if (sg.cs instanceof StrandColourScheme)
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270 strandColour.setSelected(true);
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272 else if (sg.cs instanceof TurnColourScheme)
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274 turnColour.setSelected(true);
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276 else if (sg.cs instanceof BuriedColourScheme)
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278 buriedColour.setSelected(true);
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280 else if (sg.cs instanceof ClustalxColourScheme)
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282 clustalColour.setSelected(true);
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286 noColourmenuItem.setSelected(true);
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289 if (sg.cs!=null && sg.cs.conservationApplied())
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291 conservationMenuItem.setSelected(true);
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294 showText.setSelected(sg.getDisplayText());
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295 showColourText.setSelected(sg.getColourText());
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296 showBoxes.setSelected(sg.getDisplayBoxes());
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300 groupMenu.setVisible(false);
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301 editMenu.setVisible(false);
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304 if (!ap.av.alignment.getGroups().contains(sg))
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306 unGroupMenuItem.setVisible(false);
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312 sequenceMenu.setVisible(false);
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313 pdbMenu.setVisible(false);
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316 if(links != null && links.size()>0)
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318 JMenu linkMenu = new JMenu("Link");
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320 for(int i=0; i<links.size(); i++)
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322 String link = links.elementAt(i).toString();
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323 final String label = link.substring(0, link.indexOf("|"));
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324 item = new JMenuItem(label);
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327 if (link.indexOf("$SEQUENCE_ID$") > -1)
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329 String id = seq.getName();
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330 if (id.indexOf("|") > -1)
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331 id = id.substring(id.lastIndexOf("|") + 1);
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333 url = link.substring(link.indexOf("|") + 1,
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334 link.indexOf("$SEQUENCE_ID$"))
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336 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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339 url = link.substring(link.lastIndexOf("|")+1);
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342 item.addActionListener(new java.awt.event.ActionListener()
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344 public void actionPerformed(ActionEvent e)
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350 linkMenu.add(item);
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353 sequenceMenu.add(linkMenu);
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363 * @throws Exception DOCUMENT ME!
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365 private void jbInit() throws Exception
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367 groupMenu.setText("Group");
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368 groupMenu.setText("Selection");
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369 groupName.setText("Name");
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370 groupName.addActionListener(new java.awt.event.ActionListener()
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372 public void actionPerformed(ActionEvent e)
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374 groupName_actionPerformed(e);
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377 sequenceMenu.setText("Sequence");
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378 sequenceName.setText("Edit Name/Description");
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379 sequenceName.addActionListener(new java.awt.event.ActionListener()
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381 public void actionPerformed(ActionEvent e)
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383 sequenceName_actionPerformed(e);
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386 PIDColour.setFocusPainted(false);
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387 unGroupMenuItem.setText("Remove Group");
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388 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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390 public void actionPerformed(ActionEvent e)
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392 unGroupMenuItem_actionPerformed(e);
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396 outline.setText("Border colour");
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397 outline.addActionListener(new java.awt.event.ActionListener()
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399 public void actionPerformed(ActionEvent e)
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401 outline_actionPerformed(e);
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404 nucleotideMenuItem.setText("Nucleotide");
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405 nucleotideMenuItem.addActionListener(new ActionListener()
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407 public void actionPerformed(ActionEvent e)
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409 nucleotideMenuItem_actionPerformed(e);
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412 colourMenu.setText("Group Colour");
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413 showBoxes.setText("Boxes");
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414 showBoxes.setState(true);
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415 showBoxes.addActionListener(new ActionListener()
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417 public void actionPerformed(ActionEvent e)
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419 showBoxes_actionPerformed(e);
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422 showText.setText("Text");
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423 showText.setState(true);
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424 showText.addActionListener(new ActionListener()
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426 public void actionPerformed(ActionEvent e)
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428 showText_actionPerformed(e);
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431 showColourText.setText("Colour Text");
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432 showColourText.addActionListener(new ActionListener()
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434 public void actionPerformed(ActionEvent e)
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436 showColourText_actionPerformed(e);
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439 editMenu.setText("Edit");
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440 cut.setText("Cut");
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441 cut.addActionListener(new ActionListener()
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443 public void actionPerformed(ActionEvent e)
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445 cut_actionPerformed(e);
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448 upperCase.setText("To Upper Case");
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449 upperCase.addActionListener(new ActionListener()
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451 public void actionPerformed(ActionEvent e)
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453 upperCase_actionPerformed(e);
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456 copy.setText("Copy");
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457 copy.addActionListener(new ActionListener()
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459 public void actionPerformed(ActionEvent e)
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461 copy_actionPerformed(e);
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464 lowerCase.setText("To Lower Case");
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465 lowerCase.addActionListener(new ActionListener()
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467 public void actionPerformed(ActionEvent e)
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469 lowerCase_actionPerformed(e);
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472 toggle.setText("Toggle Case");
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473 toggle.addActionListener(new ActionListener()
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475 public void actionPerformed(ActionEvent e)
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477 toggle_actionPerformed(e);
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480 pdbMenu.setText("Associate Structure with Sequence");
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481 pdbFromFile.setText("From File");
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482 pdbFromFile.addActionListener(new ActionListener()
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484 public void actionPerformed(ActionEvent e)
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486 pdbFromFile_actionPerformed(e);
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489 enterPDB.setText("Enter PDB Id");
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490 enterPDB.addActionListener(new ActionListener()
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492 public void actionPerformed(ActionEvent e)
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494 enterPDB_actionPerformed(e);
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497 discoverPDB.setText("Discover PDB ids");
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498 discoverPDB.addActionListener(new ActionListener()
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500 public void actionPerformed(ActionEvent e)
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502 discoverPDB_actionPerformed(e);
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505 outputMenu.setText("Output to Textbox...");
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506 sequenceFeature.setText("Create Sequence Feature");
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507 sequenceFeature.addActionListener(new ActionListener()
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509 public void actionPerformed(ActionEvent e)
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511 sequenceFeature_actionPerformed(e);
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517 groupMenu.add(editMenu);
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518 groupMenu.add(outputMenu);
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519 groupMenu.addSeparator();
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520 groupMenu.add(sequenceFeature);
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521 groupMenu.addSeparator();
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522 groupMenu.add(groupName);
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523 groupMenu.add(unGroupMenuItem);
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524 groupMenu.add(colourMenu);
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525 groupMenu.add(showBoxes);
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526 groupMenu.add(showText);
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527 groupMenu.add(showColourText);
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528 groupMenu.add(outline);
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529 sequenceMenu.add(sequenceName);
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530 sequenceMenu.add(pdbMenu);
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531 colourMenu.add(noColourmenuItem);
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532 colourMenu.add(clustalColour);
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533 colourMenu.add(BLOSUM62Colour);
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534 colourMenu.add(PIDColour);
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535 colourMenu.add(zappoColour);
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536 colourMenu.add(taylorColour);
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537 colourMenu.add(hydrophobicityColour);
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538 colourMenu.add(helixColour);
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539 colourMenu.add(strandColour);
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540 colourMenu.add(turnColour);
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541 colourMenu.add(buriedColour);
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542 colourMenu.add(nucleotideMenuItem);
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543 colourMenu.add(userDefinedColour);
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545 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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547 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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548 getUserColourSchemes().keys();
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550 while (userColours.hasMoreElements())
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552 JMenuItem item = new JMenuItem(userColours.
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553 nextElement().toString());
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554 item.addActionListener(new ActionListener()
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556 public void actionPerformed(ActionEvent evt)
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558 userDefinedColour_actionPerformed(evt);
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561 colourMenu.add(item);
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566 colourMenu.addSeparator();
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567 colourMenu.add(abovePIDColour);
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568 colourMenu.add(conservationMenuItem);
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569 editMenu.add(copy);
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571 editMenu.add(upperCase);
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572 editMenu.add(lowerCase);
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573 editMenu.add(toggle);
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574 pdbMenu.add(pdbFromFile);
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575 pdbMenu.add(enterPDB);
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576 pdbMenu.add(discoverPDB);
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577 noColourmenuItem.setText("None");
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578 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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580 public void actionPerformed(ActionEvent e)
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582 noColourmenuItem_actionPerformed(e);
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586 clustalColour.setText("Clustalx colours");
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587 clustalColour.addActionListener(new java.awt.event.ActionListener()
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589 public void actionPerformed(ActionEvent e)
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591 clustalColour_actionPerformed(e);
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594 zappoColour.setText("Zappo");
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595 zappoColour.addActionListener(new java.awt.event.ActionListener()
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597 public void actionPerformed(ActionEvent e)
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599 zappoColour_actionPerformed(e);
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602 taylorColour.setText("Taylor");
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603 taylorColour.addActionListener(new java.awt.event.ActionListener()
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605 public void actionPerformed(ActionEvent e)
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607 taylorColour_actionPerformed(e);
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610 hydrophobicityColour.setText("Hydrophobicity");
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611 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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613 public void actionPerformed(ActionEvent e)
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615 hydrophobicityColour_actionPerformed(e);
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618 helixColour.setText("Helix propensity");
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619 helixColour.addActionListener(new java.awt.event.ActionListener()
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621 public void actionPerformed(ActionEvent e)
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623 helixColour_actionPerformed(e);
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626 strandColour.setText("Strand propensity");
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627 strandColour.addActionListener(new java.awt.event.ActionListener()
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629 public void actionPerformed(ActionEvent e)
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631 strandColour_actionPerformed(e);
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634 turnColour.setText("Turn propensity");
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635 turnColour.addActionListener(new java.awt.event.ActionListener()
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637 public void actionPerformed(ActionEvent e)
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639 turnColour_actionPerformed(e);
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642 buriedColour.setText("Buried Index");
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643 buriedColour.addActionListener(new java.awt.event.ActionListener()
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645 public void actionPerformed(ActionEvent e)
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647 buriedColour_actionPerformed(e);
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650 abovePIDColour.setText("Above % Identity");
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651 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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653 public void actionPerformed(ActionEvent e)
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655 abovePIDColour_actionPerformed(e);
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658 userDefinedColour.setText("User Defined...");
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659 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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661 public void actionPerformed(ActionEvent e)
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663 userDefinedColour_actionPerformed(e);
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666 PIDColour.setText("Percentage Identity");
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667 PIDColour.addActionListener(new java.awt.event.ActionListener()
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669 public void actionPerformed(ActionEvent e)
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671 PIDColour_actionPerformed(e);
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674 BLOSUM62Colour.setText("BLOSUM62");
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675 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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677 public void actionPerformed(ActionEvent e)
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679 BLOSUM62Colour_actionPerformed(e);
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682 conservationMenuItem.setText("Conservation");
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683 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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685 public void actionPerformed(ActionEvent e)
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687 conservationMenuItem_actionPerformed(e);
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697 if (ap.overviewPanel != null)
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698 ap.overviewPanel.updateOverviewImage();
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700 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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706 * @param e DOCUMENT ME!
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708 protected void clustalColour_actionPerformed(ActionEvent e)
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710 SequenceGroup sg = getGroup();
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711 sg.cs = new ClustalxColourScheme(sg.getSequences(true),
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712 ap.av.alignment.getWidth());
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719 * @param e DOCUMENT ME!
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721 protected void zappoColour_actionPerformed(ActionEvent e)
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723 getGroup().cs = new ZappoColourScheme();
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730 * @param e DOCUMENT ME!
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732 protected void taylorColour_actionPerformed(ActionEvent e)
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734 getGroup().cs = new TaylorColourScheme();
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741 * @param e DOCUMENT ME!
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743 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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745 getGroup().cs = new HydrophobicColourScheme();
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752 * @param e DOCUMENT ME!
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754 protected void helixColour_actionPerformed(ActionEvent e)
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756 getGroup().cs = new HelixColourScheme();
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763 * @param e DOCUMENT ME!
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765 protected void strandColour_actionPerformed(ActionEvent e)
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767 getGroup().cs = new StrandColourScheme();
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774 * @param e DOCUMENT ME!
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776 protected void turnColour_actionPerformed(ActionEvent e)
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778 getGroup().cs = new TurnColourScheme();
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785 * @param e DOCUMENT ME!
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787 protected void buriedColour_actionPerformed(ActionEvent e)
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789 getGroup().cs = new BuriedColourScheme();
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796 * @param e DOCUMENT ME!
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798 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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800 getGroup().cs = new NucleotideColourScheme();
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807 * @param e DOCUMENT ME!
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809 protected void abovePIDColour_actionPerformed(ActionEvent e)
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811 SequenceGroup sg = getGroup();
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815 if (abovePIDColour.isSelected())
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817 sg.cs.setConsensus(AAFrequency.calculate(
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818 sg.getSequences(true), 0,
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819 ap.av.alignment.getWidth()));
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821 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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822 getGroup().getName());
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824 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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826 SliderPanel.showPIDSlider();
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828 else // remove PIDColouring
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830 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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839 * @param e DOCUMENT ME!
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841 protected void userDefinedColour_actionPerformed(ActionEvent e)
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843 SequenceGroup sg = getGroup();
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845 if (e.getActionCommand().equals("User Defined..."))
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846 new UserDefinedColours(ap, sg);
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849 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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850 getUserColourSchemes().get(e.getActionCommand());
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859 * @param e DOCUMENT ME!
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861 protected void PIDColour_actionPerformed(ActionEvent e)
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863 SequenceGroup sg = getGroup();
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864 sg.cs = new PIDColourScheme();
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865 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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866 ap.av.alignment.getWidth()));
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873 * @param e DOCUMENT ME!
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875 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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877 SequenceGroup sg = getGroup();
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879 sg.cs = new Blosum62ColourScheme();
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881 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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882 ap.av.alignment.getWidth()));
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890 * @param e DOCUMENT ME!
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892 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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894 getGroup().cs = null;
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901 * @param e DOCUMENT ME!
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903 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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905 SequenceGroup sg = getGroup();
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909 if (conservationMenuItem.isSelected())
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911 Conservation c = new Conservation("Group",
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912 ResidueProperties.propHash, 3,
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913 sg.getSequences(true), 0,
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914 ap.av.alignment.getWidth());
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917 c.verdict(false, ap.av.ConsPercGaps);
\r
919 sg.cs.setConservation(c);
\r
921 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
922 SliderPanel.showConservationSlider();
\r
924 else // remove ConservationColouring
\r
926 sg.cs.setConservation(null);
\r
935 * @param e DOCUMENT ME!
\r
937 protected void groupName_actionPerformed(ActionEvent e)
\r
939 SequenceGroup sg = getGroup();
\r
940 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
941 "Enter new group name", "Edit group name",
\r
942 JOptionPane.QUESTION_MESSAGE);
\r
950 groupName.setText(reply);
\r
956 * @param e DOCUMENT ME!
\r
958 protected void analyze_actionPerformed(ActionEvent e)
\r
960 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
961 JInternalFrame frame = new JInternalFrame();
\r
962 frame.setContentPane(cap);
\r
963 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
\r
965 SequenceGroup sg = getGroup();
\r
966 StringBuffer sb = new StringBuffer();
\r
968 for (int i = 0; i < sg.getSize(false); i++)
\r
970 Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
\r
971 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
\r
975 sb.append("Something amazing will happen soon");
\r
976 cap.setText(sb.toString());
\r
982 * @return DOCUMENT ME!
\r
984 SequenceGroup getGroup()
\r
986 SequenceGroup sg = ap.av.getSelectionGroup();
\r
987 // this method won't add a new group if it already exists
\r
989 ap.av.alignment.addGroup(sg);
\r
997 * @param e DOCUMENT ME!
\r
999 void sequenceName_actionPerformed(ActionEvent e)
\r
1001 JLabel idlabel = new JLabel( " Sequence Name ");
\r
1002 JLabel desclabel = new JLabel("Sequence Description ");
\r
1003 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
1004 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
1005 JTextField id = new JTextField(sequence.getName(), 40);
\r
1006 JTextField description = new JTextField(sequence.getDescription(), 40);
\r
1007 JPanel panel = new JPanel(new BorderLayout());
\r
1008 JPanel panel2 = new JPanel(new BorderLayout());
\r
1009 panel2.add(idlabel, BorderLayout.WEST);
\r
1010 panel2.add(id, BorderLayout.CENTER);
\r
1011 panel.add(panel2, BorderLayout.NORTH);
\r
1012 panel2 = new JPanel(new BorderLayout());
\r
1013 panel2.add(desclabel, BorderLayout.WEST);
\r
1014 panel2.add(description, BorderLayout.CENTER);
\r
1015 panel.add(panel2, BorderLayout.SOUTH);
\r
1018 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
1019 panel, "Edit Sequence Name/Description",
\r
1020 JOptionPane.OK_CANCEL_OPTION );
\r
1023 if (reply != JOptionPane.OK_OPTION )
\r
1028 String s = id.getText();
\r
1032 if (s.indexOf(" ") > -1)
\r
1034 JOptionPane.showMessageDialog(ap,
\r
1035 "Spaces have been converted to \"_\"",
\r
1036 "No spaces allowed in Sequence Name",
\r
1037 JOptionPane.WARNING_MESSAGE);
\r
1040 s = s.replace(' ', '_');
\r
1041 sequence.getDatasetSequence().setName(s);
\r
1042 sequence.setName(s);
\r
1046 sequence.getDatasetSequence().setDescription(description.getText());
\r
1047 sequence.setDescription(description.getText());
\r
1053 * @param e DOCUMENT ME!
\r
1055 void unGroupMenuItem_actionPerformed(ActionEvent e)
\r
1057 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1058 ap.av.alignment.deleteGroup(sg);
\r
1059 ap.av.setSelectionGroup(null);
\r
1067 * @param e DOCUMENT ME!
\r
1069 protected void outline_actionPerformed(ActionEvent e)
\r
1071 SequenceGroup sg = getGroup();
\r
1072 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1077 sg.setOutlineColour(col);
\r
1086 * @param e DOCUMENT ME!
\r
1088 public void showBoxes_actionPerformed(ActionEvent e)
\r
1090 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1097 * @param e DOCUMENT ME!
\r
1099 public void showText_actionPerformed(ActionEvent e)
\r
1101 getGroup().setDisplayText(showText.isSelected());
\r
1108 * @param e DOCUMENT ME!
\r
1110 public void showColourText_actionPerformed(ActionEvent e)
\r
1112 getGroup().setColourText(showColourText.isSelected());
\r
1116 public void showLink(String url)
\r
1120 jalview.util.BrowserLauncher.openURL(url);
\r
1122 catch (Exception ex)
\r
1124 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1125 "Unixers: Couldn't find default web browser."
\r
1126 +"\nAdd the full path to your browser in Preferences.",
\r
1127 "Web browser not found", JOptionPane.WARNING_MESSAGE );
\r
1130 ex.printStackTrace();
\r
1134 void hideSequences(boolean representGroup)
\r
1136 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1137 if(sg==null || sg.getSize(false)<1)
\r
1139 ap.av.hideSequence(new SequenceI[]{sequence});
\r
1143 int gsize = sg.getSize(false);
\r
1144 SequenceI [] hseqs;
\r
1146 hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
\r
1149 for(int i=0; i<gsize; i++)
\r
1151 if(representGroup && sg.getSequenceAt(i)!=sequence)
\r
1153 sequence.addHiddenSequence(sg.getSequenceAt(i));
\r
1154 hseqs[index++] = sg.getSequenceAt(i);
\r
1156 else if(!representGroup)
\r
1158 hseqs[index++] = sg.getSequenceAt(i);
\r
1162 ap.av.hideSequence(hseqs);
\r
1164 ap.av.setSelectionGroup(null);
\r
1167 public void copy_actionPerformed(ActionEvent e)
\r
1169 ap.alignFrame.copy_actionPerformed(null);
\r
1172 public void cut_actionPerformed(ActionEvent e)
\r
1174 ap.alignFrame.cut_actionPerformed(null);
\r
1177 public void upperCase_actionPerformed(ActionEvent e)
\r
1179 changeCase(e.getSource());
\r
1182 public void lowerCase_actionPerformed(ActionEvent e)
\r
1184 changeCase(e.getSource());
\r
1187 public void toggle_actionPerformed(ActionEvent e)
\r
1189 changeCase(e.getSource());
\r
1192 void changeCase(Object source)
\r
1194 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1195 Vector regions = new Vector();
\r
1198 int start = sg.getStartRes();
\r
1199 int end = sg.getEndRes() + 1;
\r
1203 if (ap.av.hasHiddenColumns)
\r
1206 start = ap.av.colSel.adjustForHiddenColumns(start);
\r
1208 end = ap.av.colSel.getHiddenBoundaryRight(start);
\r
1210 end = sg.getEndRes() + 1;
\r
1211 if (end > sg.getEndRes())
\r
1212 end = sg.getEndRes() + 1;
\r
1215 regions.addElement(new int[]
\r
1218 if (ap.av.hasHiddenColumns)
\r
1220 start = ap.av.colSel.adjustForHiddenColumns(end);
\r
1221 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
\r
1224 while (end < sg.getEndRes());
\r
1226 int[][] startEnd = new int[regions.size()][2];
\r
1227 for (int i = 0; i < regions.size(); i++)
\r
1229 startEnd[i] = (int[]) regions.elementAt(i);
\r
1233 String description;
\r
1236 if(source==toggle)
\r
1238 description = "Toggle Case";
\r
1239 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1241 else if(source==upperCase)
\r
1243 description = "To Upper Case";
\r
1244 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1248 description = "To Lower Case";
\r
1249 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1252 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1253 description, sg.getSequencesAsArray(true), startEnd, caseChange
\r
1256 ap.alignFrame.addHistoryItem(caseCommand);
\r
1259 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
\r
1263 public void outputText_actionPerformed(ActionEvent e)
\r
1265 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1266 Desktop.addInternalFrame(cap,
\r
1267 "Alignment output - " + e.getActionCommand(), 600,
\r
1270 String [] omitHidden = null;
\r
1272 if(ap.av.hasHiddenColumns)
\r
1274 System.out.println("PROMPT USER HERE");
\r
1275 omitHidden = ap.av.getViewAsString(true);
\r
1278 cap.setText(new FormatAdapter().formatSequences(
\r
1279 e.getActionCommand(),
\r
1280 ap.av.getSelectionAsNewSequence(),
\r
1285 public void pdbFromFile_actionPerformed(ActionEvent e)
\r
1287 jalview.io.JalviewFileChooser chooser
\r
1288 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1290 "LAST_DIRECTORY"));
\r
1291 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1292 chooser.setDialogTitle("Select a PDB file");
\r
1293 chooser.setToolTipText("Load a PDB file");
\r
1295 int value = chooser.showOpenDialog(null);
\r
1297 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1299 PDBEntry entry = new PDBEntry();
\r
1300 String choice = chooser.getSelectedFile().getPath();
\r
1301 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1304 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1305 jalview.io.AppletFormatAdapter.FILE);
\r
1307 if (pdbfile.id == null)
\r
1309 String reply = JOptionPane.showInternalInputDialog(
\r
1311 "Couldn't find a PDB id in the file supplied."
\r
1312 + "Please enter an Id to identify this structure.",
\r
1313 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1314 if (reply == null)
\r
1317 entry.setId(reply);
\r
1320 entry.setId(pdbfile.id);
\r
1322 catch (java.io.IOException ex)
\r
1324 ex.printStackTrace();
\r
1327 entry.setFile(choice);
\r
1328 sequence.getDatasetSequence().addPDBId(entry);
\r
1333 public void enterPDB_actionPerformed(ActionEvent e)
\r
1335 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1336 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1338 if (id != null && id.length() > 0)
\r
1340 PDBEntry entry = new PDBEntry();
\r
1342 sequence.getDatasetSequence()
\r
1347 public void discoverPDB_actionPerformed(ActionEvent e)
\r
1349 new jalview.io.DBRefFetcher(
\r
1350 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r
1353 public void sequenceFeature_actionPerformed(ActionEvent e)
\r
1355 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1359 int gSize= sg.getSize(false);
\r
1360 SequenceI [] seqs = new SequenceI[gSize];
\r
1361 SequenceFeature [] features = new SequenceFeature[gSize];
\r
1363 for (int i = 0; i < gSize; i++)
\r
1365 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1366 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1367 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1368 features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
\r
1371 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1372 .createNewFeatures(seqs, features))
\r
1374 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1375 ap.av.setShowSequenceFeatures(true);
\r
1376 ap.highlightSearchResults(null);
\r