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 sequenceMenu.setText(sequence.getName());
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147 JMenuItem menuItem;
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148 if( seq.getDatasetSequence().getPDBId() != null)
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150 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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153 while (e.hasMoreElements())
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155 final PDBEntry pdb = (PDBEntry) e.nextElement();
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157 menuItem = new JMenuItem();
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158 menuItem.setText("View PDB entry: " + pdb.getId());
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159 menuItem.addActionListener(new java.awt.event.ActionListener()
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161 public void actionPerformed(ActionEvent e)
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163 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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166 sequenceMenu.add(menuItem);
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170 menuItem = new JMenuItem("Hide Sequences");
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171 menuItem.addActionListener(new java.awt.event.ActionListener()
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173 public void actionPerformed(ActionEvent e)
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175 hideSequences(false);
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180 if(ap.av.getSelectionGroup() !=null
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181 && ap.av.getSelectionGroup().getSize(false)>1)
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183 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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184 menuItem.addActionListener(new java.awt.event.ActionListener()
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186 public void actionPerformed(ActionEvent e)
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188 hideSequences(true);
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191 sequenceMenu.add(menuItem);
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194 if (ap.av.hasHiddenRows)
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196 final int index = ap.av.alignment.findIndex(seq);
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198 if (ap.av.adjustForHiddenSeqs(index) -
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199 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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201 menuItem = new JMenuItem("Reveal Sequences");
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202 menuItem.addActionListener(new ActionListener()
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204 public void actionPerformed(ActionEvent e)
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206 ap.av.showSequence(index);
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207 if (ap.overviewPanel != null)
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208 ap.overviewPanel.updateOverviewImage();
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214 menuItem = new JMenuItem("Reveal All");
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215 menuItem.addActionListener(new ActionListener()
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217 public void actionPerformed(ActionEvent e)
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219 ap.av.showAllHiddenSeqs();
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220 if (ap.overviewPanel != null)
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221 ap.overviewPanel.updateOverviewImage();
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233 SequenceGroup sg = ap.av.getSelectionGroup();
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237 groupName.setText(sg.getName());
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239 if (sg.cs instanceof ZappoColourScheme)
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241 zappoColour.setSelected(true);
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243 else if (sg.cs instanceof TaylorColourScheme)
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245 taylorColour.setSelected(true);
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247 else if (sg.cs instanceof PIDColourScheme)
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249 PIDColour.setSelected(true);
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251 else if (sg.cs instanceof Blosum62ColourScheme)
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253 BLOSUM62Colour.setSelected(true);
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255 else if (sg.cs instanceof UserColourScheme)
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257 userDefinedColour.setSelected(true);
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259 else if (sg.cs instanceof HydrophobicColourScheme)
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261 hydrophobicityColour.setSelected(true);
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263 else if (sg.cs instanceof HelixColourScheme)
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265 helixColour.setSelected(true);
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267 else if (sg.cs instanceof StrandColourScheme)
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269 strandColour.setSelected(true);
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271 else if (sg.cs instanceof TurnColourScheme)
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273 turnColour.setSelected(true);
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275 else if (sg.cs instanceof BuriedColourScheme)
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277 buriedColour.setSelected(true);
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279 else if (sg.cs instanceof ClustalxColourScheme)
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281 clustalColour.setSelected(true);
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285 noColourmenuItem.setSelected(true);
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288 if (sg.cs!=null && sg.cs.conservationApplied())
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290 conservationMenuItem.setSelected(true);
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293 showText.setSelected(sg.getDisplayText());
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294 showColourText.setSelected(sg.getColourText());
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295 showBoxes.setSelected(sg.getDisplayBoxes());
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299 groupMenu.setVisible(false);
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300 editMenu.setVisible(false);
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303 if (!ap.av.alignment.getGroups().contains(sg))
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305 unGroupMenuItem.setVisible(false);
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311 sequenceMenu.setVisible(false);
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312 pdbMenu.setVisible(false);
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315 if(links != null && links.size()>0)
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317 JMenu linkMenu = new JMenu("Link");
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319 for(int i=0; i<links.size(); i++)
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321 String link = links.elementAt(i).toString();
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322 final String label = link.substring(0, link.indexOf("|"));
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323 item = new JMenuItem(label);
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326 if (link.indexOf("$SEQUENCE_ID$") > -1)
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328 String id = seq.getName();
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329 if (id.indexOf("|") > -1)
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330 id = id.substring(id.lastIndexOf("|") + 1);
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332 url = link.substring(link.indexOf("|") + 1,
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333 link.indexOf("$SEQUENCE_ID$"))
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335 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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338 url = link.substring(link.lastIndexOf("|")+1);
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341 item.addActionListener(new java.awt.event.ActionListener()
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343 public void actionPerformed(ActionEvent e)
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349 linkMenu.add(item);
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352 sequenceMenu.add(linkMenu);
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362 * @throws Exception DOCUMENT ME!
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364 private void jbInit() throws Exception
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366 groupMenu.setText("Group");
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367 groupMenu.setText("Selection");
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368 groupName.setText("Name");
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369 groupName.addActionListener(new java.awt.event.ActionListener()
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371 public void actionPerformed(ActionEvent e)
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373 groupName_actionPerformed(e);
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376 sequenceMenu.setText("Sequence");
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377 sequenceName.setText("Edit Name/Description");
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378 sequenceName.addActionListener(new java.awt.event.ActionListener()
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380 public void actionPerformed(ActionEvent e)
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382 sequenceName_actionPerformed(e);
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385 PIDColour.setFocusPainted(false);
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386 unGroupMenuItem.setText("Remove Group");
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387 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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389 public void actionPerformed(ActionEvent e)
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391 unGroupMenuItem_actionPerformed(e);
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395 outline.setText("Border colour");
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396 outline.addActionListener(new java.awt.event.ActionListener()
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398 public void actionPerformed(ActionEvent e)
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400 outline_actionPerformed(e);
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403 nucleotideMenuItem.setText("Nucleotide");
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404 nucleotideMenuItem.addActionListener(new ActionListener()
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406 public void actionPerformed(ActionEvent e)
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408 nucleotideMenuItem_actionPerformed(e);
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411 colourMenu.setText("Group Colour");
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412 showBoxes.setText("Boxes");
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413 showBoxes.setState(true);
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414 showBoxes.addActionListener(new ActionListener()
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416 public void actionPerformed(ActionEvent e)
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418 showBoxes_actionPerformed(e);
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421 showText.setText("Text");
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422 showText.setState(true);
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423 showText.addActionListener(new ActionListener()
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425 public void actionPerformed(ActionEvent e)
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427 showText_actionPerformed(e);
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430 showColourText.setText("Colour Text");
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431 showColourText.addActionListener(new ActionListener()
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433 public void actionPerformed(ActionEvent e)
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435 showColourText_actionPerformed(e);
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438 editMenu.setText("Edit");
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439 cut.setText("Cut");
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440 cut.addActionListener(new ActionListener()
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442 public void actionPerformed(ActionEvent e)
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444 cut_actionPerformed(e);
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447 upperCase.setText("To Upper Case");
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448 upperCase.addActionListener(new ActionListener()
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450 public void actionPerformed(ActionEvent e)
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455 copy.setText("Copy");
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456 copy.addActionListener(new ActionListener()
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458 public void actionPerformed(ActionEvent e)
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460 copy_actionPerformed(e);
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463 lowerCase.setText("To Lower Case");
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464 lowerCase.addActionListener(new ActionListener()
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466 public void actionPerformed(ActionEvent e)
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471 toggle.setText("Toggle Case");
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472 toggle.addActionListener(new ActionListener()
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474 public void actionPerformed(ActionEvent e)
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479 pdbMenu.setText("Associate Structure with Sequence");
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480 pdbFromFile.setText("From File");
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481 pdbFromFile.addActionListener(new ActionListener()
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483 public void actionPerformed(ActionEvent e)
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485 pdbFromFile_actionPerformed(e);
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488 enterPDB.setText("Enter PDB Id");
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489 enterPDB.addActionListener(new ActionListener()
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491 public void actionPerformed(ActionEvent e)
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493 enterPDB_actionPerformed(e);
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496 discoverPDB.setText("Discover PDB ids");
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497 discoverPDB.addActionListener(new ActionListener()
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499 public void actionPerformed(ActionEvent e)
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501 discoverPDB_actionPerformed(e);
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504 outputMenu.setText("Output to Textbox...");
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505 sequenceFeature.setText("Create Sequence Feature");
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506 sequenceFeature.addActionListener(new ActionListener()
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508 public void actionPerformed(ActionEvent e)
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510 sequenceFeature_actionPerformed(e);
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516 groupMenu.add(editMenu);
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517 groupMenu.add(outputMenu);
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518 groupMenu.addSeparator();
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519 groupMenu.add(sequenceFeature);
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520 groupMenu.addSeparator();
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521 groupMenu.add(groupName);
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522 groupMenu.add(unGroupMenuItem);
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523 groupMenu.add(colourMenu);
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524 groupMenu.add(showBoxes);
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525 groupMenu.add(showText);
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526 groupMenu.add(showColourText);
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527 groupMenu.add(outline);
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528 sequenceMenu.add(sequenceName);
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529 sequenceMenu.add(pdbMenu);
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530 colourMenu.add(noColourmenuItem);
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531 colourMenu.add(clustalColour);
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532 colourMenu.add(BLOSUM62Colour);
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533 colourMenu.add(PIDColour);
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534 colourMenu.add(zappoColour);
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535 colourMenu.add(taylorColour);
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536 colourMenu.add(hydrophobicityColour);
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537 colourMenu.add(helixColour);
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538 colourMenu.add(strandColour);
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539 colourMenu.add(turnColour);
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540 colourMenu.add(buriedColour);
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541 colourMenu.add(nucleotideMenuItem);
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542 colourMenu.add(userDefinedColour);
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544 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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546 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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547 getUserColourSchemes().keys();
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549 while (userColours.hasMoreElements())
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551 JMenuItem item = new JMenuItem(userColours.
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552 nextElement().toString());
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553 item.addActionListener(new ActionListener()
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555 public void actionPerformed(ActionEvent evt)
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557 userDefinedColour_actionPerformed(evt);
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560 colourMenu.add(item);
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565 colourMenu.addSeparator();
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566 colourMenu.add(abovePIDColour);
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567 colourMenu.add(conservationMenuItem);
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568 editMenu.add(copy);
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570 editMenu.add(upperCase);
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571 editMenu.add(lowerCase);
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572 editMenu.add(toggle);
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573 pdbMenu.add(pdbFromFile);
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574 pdbMenu.add(enterPDB);
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575 pdbMenu.add(discoverPDB);
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576 noColourmenuItem.setText("None");
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577 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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579 public void actionPerformed(ActionEvent e)
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581 noColourmenuItem_actionPerformed(e);
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585 clustalColour.setText("Clustalx colours");
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586 clustalColour.addActionListener(new java.awt.event.ActionListener()
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588 public void actionPerformed(ActionEvent e)
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590 clustalColour_actionPerformed(e);
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593 zappoColour.setText("Zappo");
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594 zappoColour.addActionListener(new java.awt.event.ActionListener()
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596 public void actionPerformed(ActionEvent e)
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598 zappoColour_actionPerformed(e);
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601 taylorColour.setText("Taylor");
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602 taylorColour.addActionListener(new java.awt.event.ActionListener()
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604 public void actionPerformed(ActionEvent e)
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606 taylorColour_actionPerformed(e);
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609 hydrophobicityColour.setText("Hydrophobicity");
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610 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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612 public void actionPerformed(ActionEvent e)
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614 hydrophobicityColour_actionPerformed(e);
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617 helixColour.setText("Helix propensity");
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618 helixColour.addActionListener(new java.awt.event.ActionListener()
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620 public void actionPerformed(ActionEvent e)
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622 helixColour_actionPerformed(e);
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625 strandColour.setText("Strand propensity");
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626 strandColour.addActionListener(new java.awt.event.ActionListener()
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628 public void actionPerformed(ActionEvent e)
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630 strandColour_actionPerformed(e);
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633 turnColour.setText("Turn propensity");
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634 turnColour.addActionListener(new java.awt.event.ActionListener()
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636 public void actionPerformed(ActionEvent e)
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638 turnColour_actionPerformed(e);
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641 buriedColour.setText("Buried Index");
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642 buriedColour.addActionListener(new java.awt.event.ActionListener()
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644 public void actionPerformed(ActionEvent e)
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646 buriedColour_actionPerformed(e);
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649 abovePIDColour.setText("Above % Identity");
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650 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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652 public void actionPerformed(ActionEvent e)
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654 abovePIDColour_actionPerformed(e);
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657 userDefinedColour.setText("User Defined...");
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658 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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660 public void actionPerformed(ActionEvent e)
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662 userDefinedColour_actionPerformed(e);
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665 PIDColour.setText("Percentage Identity");
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666 PIDColour.addActionListener(new java.awt.event.ActionListener()
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668 public void actionPerformed(ActionEvent e)
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670 PIDColour_actionPerformed(e);
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673 BLOSUM62Colour.setText("BLOSUM62");
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674 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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676 public void actionPerformed(ActionEvent e)
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678 BLOSUM62Colour_actionPerformed(e);
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681 conservationMenuItem.setText("Conservation");
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682 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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684 public void actionPerformed(ActionEvent e)
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686 conservationMenuItem_actionPerformed(e);
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696 if (ap.overviewPanel != null)
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697 ap.overviewPanel.updateOverviewImage();
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699 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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705 * @param e DOCUMENT ME!
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707 protected void clustalColour_actionPerformed(ActionEvent e)
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709 SequenceGroup sg = getGroup();
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710 sg.cs = new ClustalxColourScheme(sg.getSequences(true),
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711 ap.av.alignment.getWidth());
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718 * @param e DOCUMENT ME!
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720 protected void zappoColour_actionPerformed(ActionEvent e)
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722 getGroup().cs = new ZappoColourScheme();
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729 * @param e DOCUMENT ME!
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731 protected void taylorColour_actionPerformed(ActionEvent e)
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733 getGroup().cs = new TaylorColourScheme();
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740 * @param e DOCUMENT ME!
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742 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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744 getGroup().cs = new HydrophobicColourScheme();
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751 * @param e DOCUMENT ME!
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753 protected void helixColour_actionPerformed(ActionEvent e)
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755 getGroup().cs = new HelixColourScheme();
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762 * @param e DOCUMENT ME!
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764 protected void strandColour_actionPerformed(ActionEvent e)
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766 getGroup().cs = new StrandColourScheme();
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773 * @param e DOCUMENT ME!
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775 protected void turnColour_actionPerformed(ActionEvent e)
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777 getGroup().cs = new TurnColourScheme();
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784 * @param e DOCUMENT ME!
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786 protected void buriedColour_actionPerformed(ActionEvent e)
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788 getGroup().cs = new BuriedColourScheme();
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795 * @param e DOCUMENT ME!
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797 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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799 getGroup().cs = new NucleotideColourScheme();
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806 * @param e DOCUMENT ME!
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808 protected void abovePIDColour_actionPerformed(ActionEvent e)
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810 SequenceGroup sg = getGroup();
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814 if (abovePIDColour.isSelected())
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816 sg.cs.setConsensus(AAFrequency.calculate(
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817 sg.getSequences(true), 0,
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818 ap.av.alignment.getWidth()));
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820 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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821 getGroup().getName());
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823 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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825 SliderPanel.showPIDSlider();
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827 else // remove PIDColouring
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829 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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838 * @param e DOCUMENT ME!
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840 protected void userDefinedColour_actionPerformed(ActionEvent e)
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842 SequenceGroup sg = getGroup();
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844 if (e.getActionCommand().equals("User Defined..."))
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845 new UserDefinedColours(ap, sg);
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848 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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849 getUserColourSchemes().get(e.getActionCommand());
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858 * @param e DOCUMENT ME!
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860 protected void PIDColour_actionPerformed(ActionEvent e)
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862 SequenceGroup sg = getGroup();
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863 sg.cs = new PIDColourScheme();
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864 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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865 ap.av.alignment.getWidth()));
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872 * @param e DOCUMENT ME!
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874 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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876 SequenceGroup sg = getGroup();
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878 sg.cs = new Blosum62ColourScheme();
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880 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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881 ap.av.alignment.getWidth()));
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889 * @param e DOCUMENT ME!
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891 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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893 getGroup().cs = null;
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900 * @param e DOCUMENT ME!
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902 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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904 SequenceGroup sg = getGroup();
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908 if (conservationMenuItem.isSelected())
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910 Conservation c = new Conservation("Group",
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911 ResidueProperties.propHash, 3,
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912 sg.getSequences(true), 0,
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913 ap.av.alignment.getWidth());
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916 c.verdict(false, ap.av.ConsPercGaps);
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918 sg.cs.setConservation(c);
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920 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
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921 SliderPanel.showConservationSlider();
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923 else // remove ConservationColouring
\r
925 sg.cs.setConservation(null);
\r
934 * @param e DOCUMENT ME!
\r
936 protected void groupName_actionPerformed(ActionEvent e)
\r
938 SequenceGroup sg = getGroup();
\r
939 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
940 "Enter new group name", "Edit group name",
\r
941 JOptionPane.QUESTION_MESSAGE);
\r
949 groupName.setText(reply);
\r
955 * @param e DOCUMENT ME!
\r
957 protected void analyze_actionPerformed(ActionEvent e)
\r
959 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
960 JInternalFrame frame = new JInternalFrame();
\r
961 frame.setContentPane(cap);
\r
962 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
\r
964 SequenceGroup sg = getGroup();
\r
965 StringBuffer sb = new StringBuffer();
\r
967 for (int i = 0; i < sg.getSize(false); i++)
\r
969 Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
\r
970 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
\r
974 sb.append("Something amazing will happen soon");
\r
975 cap.setText(sb.toString());
\r
981 * @return DOCUMENT ME!
\r
983 SequenceGroup getGroup()
\r
985 SequenceGroup sg = ap.av.getSelectionGroup();
\r
986 // this method won't add a new group if it already exists
\r
988 ap.av.alignment.addGroup(sg);
\r
996 * @param e DOCUMENT ME!
\r
998 void sequenceName_actionPerformed(ActionEvent e)
\r
1000 JLabel idlabel = new JLabel( " Sequence Name ");
\r
1001 JLabel desclabel = new JLabel("Sequence Description ");
\r
1002 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
1003 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
1004 JTextField id = new JTextField(sequence.getName(), 40);
\r
1005 JTextField description = new JTextField(sequence.getDescription(), 40);
\r
1006 JPanel panel = new JPanel(new BorderLayout());
\r
1007 JPanel panel2 = new JPanel(new BorderLayout());
\r
1008 panel2.add(idlabel, BorderLayout.WEST);
\r
1009 panel2.add(id, BorderLayout.CENTER);
\r
1010 panel.add(panel2, BorderLayout.NORTH);
\r
1011 panel2 = new JPanel(new BorderLayout());
\r
1012 panel2.add(desclabel, BorderLayout.WEST);
\r
1013 panel2.add(description, BorderLayout.CENTER);
\r
1014 panel.add(panel2, BorderLayout.SOUTH);
\r
1017 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
1018 panel, "Edit Sequence Name/Description",
\r
1019 JOptionPane.OK_CANCEL_OPTION );
\r
1022 if (reply != JOptionPane.OK_OPTION )
\r
1027 String s = id.getText();
\r
1031 if (s.indexOf(" ") > -1)
\r
1033 JOptionPane.showMessageDialog(ap,
\r
1034 "Spaces have been converted to \"_\"",
\r
1035 "No spaces allowed in Sequence Name",
\r
1036 JOptionPane.WARNING_MESSAGE);
\r
1039 s = s.replace(' ', '_');
\r
1040 sequence.getDatasetSequence().setName(s);
\r
1041 sequence.setName(s);
\r
1045 sequence.getDatasetSequence().setDescription(description.getText());
\r
1046 sequence.setDescription(description.getText());
\r
1052 * @param e DOCUMENT ME!
\r
1054 void unGroupMenuItem_actionPerformed(ActionEvent e)
\r
1056 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1057 ap.av.alignment.deleteGroup(sg);
\r
1058 ap.av.setSelectionGroup(null);
\r
1066 * @param e DOCUMENT ME!
\r
1068 protected void outline_actionPerformed(ActionEvent e)
\r
1070 SequenceGroup sg = getGroup();
\r
1071 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1076 sg.setOutlineColour(col);
\r
1085 * @param e DOCUMENT ME!
\r
1087 public void showBoxes_actionPerformed(ActionEvent e)
\r
1089 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1096 * @param e DOCUMENT ME!
\r
1098 public void showText_actionPerformed(ActionEvent e)
\r
1100 getGroup().setDisplayText(showText.isSelected());
\r
1107 * @param e DOCUMENT ME!
\r
1109 public void showColourText_actionPerformed(ActionEvent e)
\r
1111 getGroup().setColourText(showColourText.isSelected());
\r
1115 public void showLink(String url)
\r
1119 jalview.util.BrowserLauncher.openURL(url);
\r
1121 catch (Exception ex)
\r
1123 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1124 "Unixers: Couldn't find default web browser."
\r
1125 +"\nAdd the full path to your browser in Preferences.",
\r
1126 "Web browser not found", JOptionPane.WARNING_MESSAGE );
\r
1129 ex.printStackTrace();
\r
1133 void hideSequences(boolean representGroup)
\r
1135 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1136 if(sg==null || sg.getSize(false)<1)
\r
1138 ap.av.hideSequence(new SequenceI[]{sequence});
\r
1142 int gsize = sg.getSize(false);
\r
1143 SequenceI [] hseqs;
\r
1145 hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
\r
1148 for(int i=0; i<gsize; i++)
\r
1150 if(representGroup && sg.getSequenceAt(i)!=sequence)
\r
1152 sequence.addHiddenSequence(sg.getSequenceAt(i));
\r
1153 hseqs[index++] = sg.getSequenceAt(i);
\r
1155 else if(!representGroup)
\r
1157 hseqs[index++] = sg.getSequenceAt(i);
\r
1161 ap.av.hideSequence(hseqs);
\r
1163 ap.av.setSelectionGroup(null);
\r
1166 public void copy_actionPerformed(ActionEvent e)
\r
1168 ap.alignFrame.copy_actionPerformed(null);
\r
1171 public void cut_actionPerformed(ActionEvent e)
\r
1173 ap.alignFrame.cut_actionPerformed(null);
\r
1176 void changeCase(ActionEvent e)
\r
1178 Object source = e.getSource();
\r
1179 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1180 Vector regions = new Vector();
\r
1183 int start = sg.getStartRes();
\r
1184 int end = sg.getEndRes() + 1;
\r
1188 if (ap.av.hasHiddenColumns)
\r
1191 start = ap.av.colSel.adjustForHiddenColumns(start);
\r
1193 end = ap.av.colSel.getHiddenBoundaryRight(start);
\r
1195 end = sg.getEndRes() + 1;
\r
1196 if (end > sg.getEndRes())
\r
1197 end = sg.getEndRes() + 1;
\r
1200 regions.addElement(new int[]
\r
1203 if (ap.av.hasHiddenColumns)
\r
1205 start = ap.av.colSel.adjustForHiddenColumns(end);
\r
1206 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
\r
1209 while (end < sg.getEndRes());
\r
1211 int[][] startEnd = new int[regions.size()][2];
\r
1212 for (int i = 0; i < regions.size(); i++)
\r
1214 startEnd[i] = (int[]) regions.elementAt(i);
\r
1218 String description;
\r
1221 if(source==toggle)
\r
1223 description = "Toggle Case";
\r
1224 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1226 else if(source==upperCase)
\r
1228 description = "To Upper Case";
\r
1229 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1233 description = "To Lower Case";
\r
1234 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1237 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1238 description, sg.getSequencesAsArray(true), startEnd, caseChange
\r
1241 ap.alignFrame.addHistoryItem(caseCommand);
\r
1244 ap.av.firePropertyChange("alignment", null,
\r
1245 ap.av.getAlignment().getSequences());
\r
1250 public void outputText_actionPerformed(ActionEvent e)
\r
1252 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1253 Desktop.addInternalFrame(cap,
\r
1254 "Alignment output - " + e.getActionCommand(), 600,
\r
1257 String [] omitHidden = null;
\r
1259 if(ap.av.hasHiddenColumns)
\r
1261 System.out.println("PROMPT USER HERE");
\r
1262 omitHidden = ap.av.getViewAsString(true);
\r
1265 cap.setText(new FormatAdapter().formatSequences(
\r
1266 e.getActionCommand(),
\r
1267 ap.av.getSelectionAsNewSequence(),
\r
1272 public void pdbFromFile_actionPerformed(ActionEvent e)
\r
1274 jalview.io.JalviewFileChooser chooser
\r
1275 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1277 "LAST_DIRECTORY"));
\r
1278 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1279 chooser.setDialogTitle("Select a PDB file");
\r
1280 chooser.setToolTipText("Load a PDB file");
\r
1282 int value = chooser.showOpenDialog(null);
\r
1284 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1286 PDBEntry entry = new PDBEntry();
\r
1287 String choice = chooser.getSelectedFile().getPath();
\r
1288 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1291 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1292 jalview.io.AppletFormatAdapter.FILE);
\r
1294 if (pdbfile.id == null)
\r
1296 String reply = JOptionPane.showInternalInputDialog(
\r
1298 "Couldn't find a PDB id in the file supplied."
\r
1299 + "Please enter an Id to identify this structure.",
\r
1300 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1301 if (reply == null)
\r
1304 entry.setId(reply);
\r
1307 entry.setId(pdbfile.id);
\r
1309 catch (java.io.IOException ex)
\r
1311 ex.printStackTrace();
\r
1314 entry.setFile(choice);
\r
1315 sequence.getDatasetSequence().addPDBId(entry);
\r
1320 public void enterPDB_actionPerformed(ActionEvent e)
\r
1322 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1323 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1325 if (id != null && id.length() > 0)
\r
1327 PDBEntry entry = new PDBEntry();
\r
1329 sequence.getDatasetSequence()
\r
1334 public void discoverPDB_actionPerformed(ActionEvent e)
\r
1336 new jalview.io.DBRefFetcher(
\r
1337 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r
1340 public void sequenceFeature_actionPerformed(ActionEvent e)
\r
1342 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1346 int gSize= sg.getSize(false);
\r
1347 SequenceI [] seqs = new SequenceI[gSize];
\r
1348 SequenceFeature [] features = new SequenceFeature[gSize];
\r
1350 for (int i = 0; i < gSize; i++)
\r
1352 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1353 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1354 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1355 features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
\r
1358 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1359 .createNewFeatures(seqs, features))
\r
1361 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1362 ap.av.setShowSequenceFeatures(true);
\r
1363 ap.highlightSearchResults(null);
\r