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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84 JMenuItem textColour = new JMenuItem();
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85 JMenu jMenu1 = new JMenu();
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88 * Creates a new PopupMenu object.
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90 * @param ap DOCUMENT ME!
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91 * @param seq DOCUMENT ME!
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93 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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95 ///////////////////////////////////////////////////////////
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96 // If this is activated from the sequence panel, the user may want to
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97 // edit or annotate a particular residue. Therefore display the residue menu
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99 // If from the IDPanel, we must display the sequence menu
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100 //////////////////////////////////////////////////////////
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104 ButtonGroup colours = new ButtonGroup();
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105 colours.add(noColourmenuItem);
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106 colours.add(clustalColour);
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107 colours.add(zappoColour);
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108 colours.add(taylorColour);
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109 colours.add(hydrophobicityColour);
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110 colours.add(helixColour);
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111 colours.add(strandColour);
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112 colours.add(turnColour);
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113 colours.add(buriedColour);
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114 colours.add(abovePIDColour);
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115 colours.add(userDefinedColour);
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116 colours.add(PIDColour);
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117 colours.add(BLOSUM62Colour);
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119 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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121 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
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123 item.addActionListener(new java.awt.event.ActionListener()
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125 public void actionPerformed(ActionEvent e)
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127 outputText_actionPerformed(e);
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131 outputMenu.add(item);
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139 catch (Exception e)
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141 e.printStackTrace();
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147 sequenceMenu.setText(sequence.getName());
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149 JMenuItem menuItem;
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150 if( seq.getDatasetSequence().getPDBId() != null)
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152 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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155 while (e.hasMoreElements())
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157 final PDBEntry pdb = (PDBEntry) e.nextElement();
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159 menuItem = new JMenuItem();
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160 menuItem.setText("View PDB entry: " + pdb.getId());
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161 menuItem.addActionListener(new java.awt.event.ActionListener()
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163 public void actionPerformed(ActionEvent e)
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165 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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168 sequenceMenu.add(menuItem);
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172 menuItem = new JMenuItem("Hide Sequences");
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173 menuItem.addActionListener(new java.awt.event.ActionListener()
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175 public void actionPerformed(ActionEvent e)
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177 hideSequences(false);
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182 if(ap.av.getSelectionGroup() !=null
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183 && ap.av.getSelectionGroup().getSize()>1)
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185 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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186 menuItem.addActionListener(new java.awt.event.ActionListener()
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188 public void actionPerformed(ActionEvent e)
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190 hideSequences(true);
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193 sequenceMenu.add(menuItem);
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196 if (ap.av.hasHiddenRows)
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198 final int index = ap.av.alignment.findIndex(seq);
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200 if (ap.av.adjustForHiddenSeqs(index) -
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201 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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203 menuItem = new JMenuItem("Reveal Sequences");
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204 menuItem.addActionListener(new ActionListener()
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206 public void actionPerformed(ActionEvent e)
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208 ap.av.showSequence(index);
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209 if (ap.overviewPanel != null)
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210 ap.overviewPanel.updateOverviewImage();
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216 menuItem = new JMenuItem("Reveal All");
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217 menuItem.addActionListener(new ActionListener()
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219 public void actionPerformed(ActionEvent e)
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221 ap.av.showAllHiddenSeqs();
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222 if (ap.overviewPanel != null)
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223 ap.overviewPanel.updateOverviewImage();
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235 SequenceGroup sg = ap.av.getSelectionGroup();
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239 groupName.setText(sg.getName());
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241 if (sg.cs instanceof ZappoColourScheme)
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243 zappoColour.setSelected(true);
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245 else if (sg.cs instanceof TaylorColourScheme)
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247 taylorColour.setSelected(true);
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249 else if (sg.cs instanceof PIDColourScheme)
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251 PIDColour.setSelected(true);
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253 else if (sg.cs instanceof Blosum62ColourScheme)
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255 BLOSUM62Colour.setSelected(true);
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257 else if (sg.cs instanceof UserColourScheme)
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259 userDefinedColour.setSelected(true);
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261 else if (sg.cs instanceof HydrophobicColourScheme)
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263 hydrophobicityColour.setSelected(true);
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265 else if (sg.cs instanceof HelixColourScheme)
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267 helixColour.setSelected(true);
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269 else if (sg.cs instanceof StrandColourScheme)
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271 strandColour.setSelected(true);
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273 else if (sg.cs instanceof TurnColourScheme)
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275 turnColour.setSelected(true);
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277 else if (sg.cs instanceof BuriedColourScheme)
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279 buriedColour.setSelected(true);
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281 else if (sg.cs instanceof ClustalxColourScheme)
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283 clustalColour.setSelected(true);
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287 noColourmenuItem.setSelected(true);
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290 if (sg.cs!=null && sg.cs.conservationApplied())
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292 conservationMenuItem.setSelected(true);
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295 showText.setSelected(sg.getDisplayText());
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296 showColourText.setSelected(sg.getColourText());
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297 showBoxes.setSelected(sg.getDisplayBoxes());
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301 groupMenu.setVisible(false);
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302 editMenu.setVisible(false);
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305 if (!ap.av.alignment.getGroups().contains(sg))
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307 unGroupMenuItem.setVisible(false);
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313 sequenceMenu.setVisible(false);
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314 pdbMenu.setVisible(false);
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317 if(links != null && links.size()>0)
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319 JMenu linkMenu = new JMenu("Link");
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321 for(int i=0; i<links.size(); i++)
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323 String link = links.elementAt(i).toString();
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324 final String label = link.substring(0, link.indexOf("|"));
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325 item = new JMenuItem(label);
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328 if (link.indexOf("$SEQUENCE_ID$") > -1)
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330 String id = seq.getName();
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331 if (id.indexOf("|") > -1)
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332 id = id.substring(id.lastIndexOf("|") + 1);
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334 url = link.substring(link.indexOf("|") + 1,
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335 link.indexOf("$SEQUENCE_ID$"))
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337 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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340 url = link.substring(link.lastIndexOf("|")+1);
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343 item.addActionListener(new java.awt.event.ActionListener()
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345 public void actionPerformed(ActionEvent e)
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351 linkMenu.add(item);
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354 sequenceMenu.add(linkMenu);
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364 * @throws Exception DOCUMENT ME!
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366 private void jbInit() throws Exception
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368 groupMenu.setText("Group");
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369 groupMenu.setText("Selection");
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370 groupName.setText("Name");
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371 groupName.addActionListener(new java.awt.event.ActionListener()
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373 public void actionPerformed(ActionEvent e)
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375 groupName_actionPerformed(e);
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378 sequenceMenu.setText("Sequence");
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379 sequenceName.setText("Edit Name/Description");
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380 sequenceName.addActionListener(new java.awt.event.ActionListener()
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382 public void actionPerformed(ActionEvent e)
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384 sequenceName_actionPerformed(e);
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387 PIDColour.setFocusPainted(false);
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388 unGroupMenuItem.setText("Remove Group");
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389 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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391 public void actionPerformed(ActionEvent e)
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393 unGroupMenuItem_actionPerformed(e);
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397 outline.setText("Border colour");
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398 outline.addActionListener(new java.awt.event.ActionListener()
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400 public void actionPerformed(ActionEvent e)
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402 outline_actionPerformed(e);
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405 nucleotideMenuItem.setText("Nucleotide");
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406 nucleotideMenuItem.addActionListener(new ActionListener()
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408 public void actionPerformed(ActionEvent e)
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410 nucleotideMenuItem_actionPerformed(e);
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413 colourMenu.setText("Group Colour");
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414 showBoxes.setText("Boxes");
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415 showBoxes.setState(true);
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416 showBoxes.addActionListener(new ActionListener()
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418 public void actionPerformed(ActionEvent e)
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420 showBoxes_actionPerformed(e);
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423 showText.setText("Text");
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424 showText.setState(true);
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425 showText.addActionListener(new ActionListener()
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427 public void actionPerformed(ActionEvent e)
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429 showText_actionPerformed(e);
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432 showColourText.setText("Colour Text");
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433 showColourText.addActionListener(new ActionListener()
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435 public void actionPerformed(ActionEvent e)
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437 showColourText_actionPerformed(e);
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440 editMenu.setText("Edit");
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441 cut.setText("Cut");
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442 cut.addActionListener(new ActionListener()
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444 public void actionPerformed(ActionEvent e)
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446 cut_actionPerformed(e);
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449 upperCase.setText("To Upper Case");
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450 upperCase.addActionListener(new ActionListener()
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452 public void actionPerformed(ActionEvent e)
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457 copy.setText("Copy");
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458 copy.addActionListener(new ActionListener()
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460 public void actionPerformed(ActionEvent e)
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462 copy_actionPerformed(e);
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465 lowerCase.setText("To Lower Case");
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466 lowerCase.addActionListener(new ActionListener()
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468 public void actionPerformed(ActionEvent e)
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473 toggle.setText("Toggle Case");
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474 toggle.addActionListener(new ActionListener()
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476 public void actionPerformed(ActionEvent e)
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481 pdbMenu.setText("Associate Structure with Sequence");
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482 pdbFromFile.setText("From File");
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483 pdbFromFile.addActionListener(new ActionListener()
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485 public void actionPerformed(ActionEvent e)
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487 pdbFromFile_actionPerformed(e);
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490 enterPDB.setText("Enter PDB Id");
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491 enterPDB.addActionListener(new ActionListener()
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493 public void actionPerformed(ActionEvent e)
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495 enterPDB_actionPerformed(e);
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498 discoverPDB.setText("Discover PDB ids");
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499 discoverPDB.addActionListener(new ActionListener()
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501 public void actionPerformed(ActionEvent e)
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503 discoverPDB_actionPerformed(e);
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506 outputMenu.setText("Output to Textbox...");
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507 sequenceFeature.setText("Create Sequence Feature");
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508 sequenceFeature.addActionListener(new ActionListener()
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510 public void actionPerformed(ActionEvent e)
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512 sequenceFeature_actionPerformed(e);
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515 textColour.setText("Text Colour");
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516 textColour.addActionListener(new ActionListener()
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518 public void actionPerformed(ActionEvent e)
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520 textColour_actionPerformed(e);
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523 jMenu1.setText("Group");
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527 groupMenu.add(editMenu);
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528 groupMenu.add(outputMenu);
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529 groupMenu.add(sequenceFeature);
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530 groupMenu.add(jMenu1);
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531 sequenceMenu.add(sequenceName);
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532 sequenceMenu.add(pdbMenu);
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533 colourMenu.add(textColour);
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534 colourMenu.add(noColourmenuItem);
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535 colourMenu.add(clustalColour);
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536 colourMenu.add(BLOSUM62Colour);
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537 colourMenu.add(PIDColour);
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538 colourMenu.add(zappoColour);
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539 colourMenu.add(taylorColour);
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540 colourMenu.add(hydrophobicityColour);
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541 colourMenu.add(helixColour);
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542 colourMenu.add(strandColour);
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543 colourMenu.add(turnColour);
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544 colourMenu.add(buriedColour);
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545 colourMenu.add(nucleotideMenuItem);
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546 colourMenu.add(userDefinedColour);
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548 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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550 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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551 getUserColourSchemes().keys();
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553 while (userColours.hasMoreElements())
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555 JMenuItem item = new JMenuItem(userColours.
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556 nextElement().toString());
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557 item.addActionListener(new ActionListener()
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559 public void actionPerformed(ActionEvent evt)
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561 userDefinedColour_actionPerformed(evt);
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564 colourMenu.add(item);
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569 colourMenu.addSeparator();
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570 colourMenu.add(abovePIDColour);
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571 colourMenu.add(conservationMenuItem);
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572 editMenu.add(copy);
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574 editMenu.add(upperCase);
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575 editMenu.add(lowerCase);
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576 editMenu.add(toggle);
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577 pdbMenu.add(pdbFromFile);
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578 pdbMenu.add(enterPDB);
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579 pdbMenu.add(discoverPDB);
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580 jMenu1.add(groupName);
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581 jMenu1.add(unGroupMenuItem);
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582 jMenu1.add(colourMenu);
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583 jMenu1.add(showBoxes);
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584 jMenu1.add(showText);
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585 jMenu1.add(showColourText);
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586 jMenu1.add(outline);
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587 noColourmenuItem.setText("None");
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588 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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590 public void actionPerformed(ActionEvent e)
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592 noColourmenuItem_actionPerformed(e);
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596 clustalColour.setText("Clustalx colours");
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597 clustalColour.addActionListener(new java.awt.event.ActionListener()
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599 public void actionPerformed(ActionEvent e)
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601 clustalColour_actionPerformed(e);
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604 zappoColour.setText("Zappo");
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605 zappoColour.addActionListener(new java.awt.event.ActionListener()
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607 public void actionPerformed(ActionEvent e)
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609 zappoColour_actionPerformed(e);
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612 taylorColour.setText("Taylor");
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613 taylorColour.addActionListener(new java.awt.event.ActionListener()
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615 public void actionPerformed(ActionEvent e)
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617 taylorColour_actionPerformed(e);
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620 hydrophobicityColour.setText("Hydrophobicity");
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621 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 hydrophobicityColour_actionPerformed(e);
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628 helixColour.setText("Helix propensity");
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629 helixColour.addActionListener(new java.awt.event.ActionListener()
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631 public void actionPerformed(ActionEvent e)
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633 helixColour_actionPerformed(e);
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636 strandColour.setText("Strand propensity");
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637 strandColour.addActionListener(new java.awt.event.ActionListener()
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639 public void actionPerformed(ActionEvent e)
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641 strandColour_actionPerformed(e);
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644 turnColour.setText("Turn propensity");
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645 turnColour.addActionListener(new java.awt.event.ActionListener()
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647 public void actionPerformed(ActionEvent e)
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649 turnColour_actionPerformed(e);
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652 buriedColour.setText("Buried Index");
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653 buriedColour.addActionListener(new java.awt.event.ActionListener()
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655 public void actionPerformed(ActionEvent e)
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657 buriedColour_actionPerformed(e);
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660 abovePIDColour.setText("Above % Identity");
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661 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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663 public void actionPerformed(ActionEvent e)
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665 abovePIDColour_actionPerformed(e);
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668 userDefinedColour.setText("User Defined...");
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669 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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671 public void actionPerformed(ActionEvent e)
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673 userDefinedColour_actionPerformed(e);
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676 PIDColour.setText("Percentage Identity");
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677 PIDColour.addActionListener(new java.awt.event.ActionListener()
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679 public void actionPerformed(ActionEvent e)
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681 PIDColour_actionPerformed(e);
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684 BLOSUM62Colour.setText("BLOSUM62");
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685 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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687 public void actionPerformed(ActionEvent e)
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689 BLOSUM62Colour_actionPerformed(e);
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692 conservationMenuItem.setText("Conservation");
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693 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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695 public void actionPerformed(ActionEvent e)
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697 conservationMenuItem_actionPerformed(e);
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707 if (ap.overviewPanel != null)
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708 ap.overviewPanel.updateOverviewImage();
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710 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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716 * @param e DOCUMENT ME!
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718 protected void clustalColour_actionPerformed(ActionEvent e)
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720 SequenceGroup sg = getGroup();
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721 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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722 ap.av.alignment.getWidth());
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729 * @param e DOCUMENT ME!
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731 protected void zappoColour_actionPerformed(ActionEvent e)
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733 getGroup().cs = new ZappoColourScheme();
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740 * @param e DOCUMENT ME!
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742 protected void taylorColour_actionPerformed(ActionEvent e)
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744 getGroup().cs = new TaylorColourScheme();
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751 * @param e DOCUMENT ME!
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753 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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755 getGroup().cs = new HydrophobicColourScheme();
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762 * @param e DOCUMENT ME!
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764 protected void helixColour_actionPerformed(ActionEvent e)
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766 getGroup().cs = new HelixColourScheme();
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773 * @param e DOCUMENT ME!
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775 protected void strandColour_actionPerformed(ActionEvent e)
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777 getGroup().cs = new StrandColourScheme();
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784 * @param e DOCUMENT ME!
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786 protected void turnColour_actionPerformed(ActionEvent e)
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788 getGroup().cs = new TurnColourScheme();
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795 * @param e DOCUMENT ME!
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797 protected void buriedColour_actionPerformed(ActionEvent e)
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799 getGroup().cs = new BuriedColourScheme();
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806 * @param e DOCUMENT ME!
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808 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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810 getGroup().cs = new NucleotideColourScheme();
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817 * @param e DOCUMENT ME!
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819 protected void abovePIDColour_actionPerformed(ActionEvent e)
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821 SequenceGroup sg = getGroup();
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825 if (abovePIDColour.isSelected())
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827 sg.cs.setConsensus(AAFrequency.calculate(
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828 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
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829 sg.getEndRes() + 1));
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831 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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832 getGroup().getName());
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834 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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836 SliderPanel.showPIDSlider();
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838 else // remove PIDColouring
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840 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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849 * @param e DOCUMENT ME!
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851 protected void userDefinedColour_actionPerformed(ActionEvent e)
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853 SequenceGroup sg = getGroup();
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855 if (e.getActionCommand().equals("User Defined..."))
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856 new UserDefinedColours(ap, sg);
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859 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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860 getUserColourSchemes().get(e.getActionCommand());
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869 * @param e DOCUMENT ME!
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871 protected void PIDColour_actionPerformed(ActionEvent e)
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873 SequenceGroup sg = getGroup();
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874 sg.cs = new PIDColourScheme();
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875 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
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877 sg.getEndRes() + 1));
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884 * @param e DOCUMENT ME!
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886 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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888 SequenceGroup sg = getGroup();
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890 sg.cs = new Blosum62ColourScheme();
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892 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
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894 sg.getEndRes() + 1));
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902 * @param e DOCUMENT ME!
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904 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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906 getGroup().cs = null;
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913 * @param e DOCUMENT ME!
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915 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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917 SequenceGroup sg = getGroup();
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921 if (conservationMenuItem.isSelected())
\r
923 Conservation c = new Conservation("Group",
\r
924 ResidueProperties.propHash, 3,
\r
925 sg.getSequences(ap.av.hiddenRepSequences),
\r
927 sg.getEndRes() + 1);
\r
930 c.verdict(false, ap.av.ConsPercGaps);
\r
932 sg.cs.setConservation(c);
\r
934 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
935 SliderPanel.showConservationSlider();
\r
937 else // remove ConservationColouring
\r
939 sg.cs.setConservation(null);
\r
948 * @param e DOCUMENT ME!
\r
950 protected void groupName_actionPerformed(ActionEvent e)
\r
952 SequenceGroup sg = getGroup();
\r
953 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
954 "Enter new group name", "Edit group name",
\r
955 JOptionPane.QUESTION_MESSAGE);
\r
963 groupName.setText(reply);
\r
970 * @return DOCUMENT ME!
\r
972 SequenceGroup getGroup()
\r
974 SequenceGroup sg = ap.av.getSelectionGroup();
\r
975 // this method won't add a new group if it already exists
\r
977 ap.av.alignment.addGroup(sg);
\r
985 * @param e DOCUMENT ME!
\r
987 void sequenceName_actionPerformed(ActionEvent e)
\r
989 JLabel idlabel = new JLabel( " Sequence Name ");
\r
990 JLabel desclabel = new JLabel("Sequence Description ");
\r
991 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
992 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
993 JTextField id = new JTextField(sequence.getName(), 40);
\r
994 JTextField description = new JTextField(sequence.getDescription(), 40);
\r
995 JPanel panel = new JPanel(new BorderLayout());
\r
996 JPanel panel2 = new JPanel(new BorderLayout());
\r
997 panel2.add(idlabel, BorderLayout.WEST);
\r
998 panel2.add(id, BorderLayout.CENTER);
\r
999 panel.add(panel2, BorderLayout.NORTH);
\r
1000 panel2 = new JPanel(new BorderLayout());
\r
1001 panel2.add(desclabel, BorderLayout.WEST);
\r
1002 panel2.add(description, BorderLayout.CENTER);
\r
1003 panel.add(panel2, BorderLayout.SOUTH);
\r
1006 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
1007 panel, "Edit Sequence Name/Description",
\r
1008 JOptionPane.OK_CANCEL_OPTION );
\r
1011 if (reply != JOptionPane.OK_OPTION )
\r
1016 String s = id.getText();
\r
1020 if (s.indexOf(" ") > -1)
\r
1022 JOptionPane.showMessageDialog(ap,
\r
1023 "Spaces have been converted to \"_\"",
\r
1024 "No spaces allowed in Sequence Name",
\r
1025 JOptionPane.WARNING_MESSAGE);
\r
1028 s = s.replace(' ', '_');
\r
1029 sequence.setName(s);
\r
1033 sequence.setDescription(description.getText());
\r
1035 ap.av.firePropertyChange("alignment", null,
\r
1036 ap.av.getAlignment().getSequences());
\r
1043 * @param e DOCUMENT ME!
\r
1045 void unGroupMenuItem_actionPerformed(ActionEvent e)
\r
1047 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1048 ap.av.alignment.deleteGroup(sg);
\r
1049 ap.av.setSelectionGroup(null);
\r
1057 * @param e DOCUMENT ME!
\r
1059 protected void outline_actionPerformed(ActionEvent e)
\r
1061 SequenceGroup sg = getGroup();
\r
1062 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1067 sg.setOutlineColour(col);
\r
1076 * @param e DOCUMENT ME!
\r
1078 public void showBoxes_actionPerformed(ActionEvent e)
\r
1080 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1087 * @param e DOCUMENT ME!
\r
1089 public void showText_actionPerformed(ActionEvent e)
\r
1091 getGroup().setDisplayText(showText.isSelected());
\r
1098 * @param e DOCUMENT ME!
\r
1100 public void showColourText_actionPerformed(ActionEvent e)
\r
1102 getGroup().setColourText(showColourText.isSelected());
\r
1106 public void showLink(String url)
\r
1110 jalview.util.BrowserLauncher.openURL(url);
\r
1112 catch (Exception ex)
\r
1114 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1115 "Unixers: Couldn't find default web browser."
\r
1116 +"\nAdd the full path to your browser in Preferences.",
\r
1117 "Web browser not found", JOptionPane.WARNING_MESSAGE );
\r
1120 ex.printStackTrace();
\r
1124 void hideSequences(boolean representGroup)
\r
1126 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1127 if(sg==null || sg.getSize()<1)
\r
1129 ap.av.hideSequence(new SequenceI[]{sequence});
\r
1133 ap.av.setSelectionGroup(null);
\r
1135 if (representGroup)
\r
1137 ap.av.hideRepSequences(sequence, sg);
\r
1142 int gsize = sg.getSize();
\r
1143 SequenceI[] hseqs;
\r
1145 hseqs = new SequenceI[gsize];
\r
1148 for (int i = 0; i < gsize; i++)
\r
1150 hseqs[index++] = sg.getSequenceAt(i);
\r
1153 ap.av.hideSequence(hseqs);
\r
1156 public void copy_actionPerformed(ActionEvent e)
\r
1158 ap.alignFrame.copy_actionPerformed(null);
\r
1161 public void cut_actionPerformed(ActionEvent e)
\r
1163 ap.alignFrame.cut_actionPerformed(null);
\r
1166 void changeCase(ActionEvent e)
\r
1168 Object source = e.getSource();
\r
1169 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1170 Vector regions = new Vector();
\r
1173 int start = sg.getStartRes();
\r
1174 int end = sg.getEndRes() + 1;
\r
1178 if (ap.av.hasHiddenColumns)
\r
1181 start = ap.av.colSel.adjustForHiddenColumns(start);
\r
1183 end = ap.av.colSel.getHiddenBoundaryRight(start);
\r
1185 end = sg.getEndRes() + 1;
\r
1186 if (end > sg.getEndRes())
\r
1187 end = sg.getEndRes() + 1;
\r
1190 regions.addElement(new int[]
\r
1193 if (ap.av.hasHiddenColumns)
\r
1195 start = ap.av.colSel.adjustForHiddenColumns(end);
\r
1196 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
\r
1199 while (end < sg.getEndRes());
\r
1201 int[][] startEnd = new int[regions.size()][2];
\r
1202 for (int i = 0; i < regions.size(); i++)
\r
1204 startEnd[i] = (int[]) regions.elementAt(i);
\r
1208 String description;
\r
1211 if(source==toggle)
\r
1213 description = "Toggle Case";
\r
1214 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1216 else if(source==upperCase)
\r
1218 description = "To Upper Case";
\r
1219 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1223 description = "To Lower Case";
\r
1224 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1227 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1228 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1229 startEnd, caseChange
\r
1232 ap.alignFrame.addHistoryItem(caseCommand);
\r
1235 ap.av.firePropertyChange("alignment", null,
\r
1236 ap.av.getAlignment().getSequences());
\r
1241 public void outputText_actionPerformed(ActionEvent e)
\r
1243 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1244 cap.setForInput(null);
\r
1245 Desktop.addInternalFrame(cap,
\r
1246 "Alignment output - " + e.getActionCommand(), 600,
\r
1249 String [] omitHidden = null;
\r
1251 if(ap.av.hasHiddenColumns)
\r
1253 System.out.println("PROMPT USER HERE");
\r
1254 omitHidden = ap.av.getViewAsString(true);
\r
1257 cap.setText(new FormatAdapter().formatSequences(
\r
1258 e.getActionCommand(),
\r
1259 ap.av.getSelectionAsNewSequence(),
\r
1264 public void pdbFromFile_actionPerformed(ActionEvent e)
\r
1266 jalview.io.JalviewFileChooser chooser
\r
1267 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1269 "LAST_DIRECTORY"));
\r
1270 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1271 chooser.setDialogTitle("Select a PDB file");
\r
1272 chooser.setToolTipText("Load a PDB file");
\r
1274 int value = chooser.showOpenDialog(null);
\r
1276 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1278 PDBEntry entry = new PDBEntry();
\r
1279 String choice = chooser.getSelectedFile().getPath();
\r
1280 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1283 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1284 jalview.io.AppletFormatAdapter.FILE);
\r
1286 if (pdbfile.id == null)
\r
1288 String reply = JOptionPane.showInternalInputDialog(
\r
1290 "Couldn't find a PDB id in the file supplied."
\r
1291 + "Please enter an Id to identify this structure.",
\r
1292 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1293 if (reply == null)
\r
1296 entry.setId(reply);
\r
1299 entry.setId(pdbfile.id);
\r
1301 catch (java.io.IOException ex)
\r
1303 ex.printStackTrace();
\r
1306 entry.setFile(choice);
\r
1307 sequence.getDatasetSequence().addPDBId(entry);
\r
1312 public void enterPDB_actionPerformed(ActionEvent e)
\r
1314 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1315 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1317 if (id != null && id.length() > 0)
\r
1319 PDBEntry entry = new PDBEntry();
\r
1321 sequence.getDatasetSequence()
\r
1326 public void discoverPDB_actionPerformed(ActionEvent e)
\r
1328 new jalview.io.DBRefFetcher(
\r
1329 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r
1332 public void sequenceFeature_actionPerformed(ActionEvent e)
\r
1334 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1338 int gSize= sg.getSize();
\r
1339 SequenceI [] seqs = new SequenceI[gSize];
\r
1340 SequenceFeature [] features = new SequenceFeature[gSize];
\r
1342 for (int i = 0; i < gSize; i++)
\r
1344 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1345 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1346 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1347 features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
\r
1350 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1351 .createNewFeatures(seqs, features))
\r
1353 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1354 ap.av.setShowSequenceFeatures(true);
\r
1355 ap.highlightSearchResults(null);
\r
1359 public void textColour_actionPerformed(ActionEvent e)
\r
1361 SequenceGroup sg = getGroup();
\r
1363 new TextColourChooser().chooseColour(ap, sg);
\r