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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25 import jalview.datamodel.*;
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28 import jalview.schemes.*;
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31 import java.awt.event.*;
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33 import javax.swing.*;
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35 import java.util.Vector;
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36 import jalview.io.FormatAdapter;
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43 * @version $Revision$
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45 public class PopupMenu extends JPopupMenu
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47 JMenu groupMenu = new JMenu();
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48 JMenuItem groupName = new JMenuItem();
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49 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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54 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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55 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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57 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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58 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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59 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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60 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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61 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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62 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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64 JMenu sequenceMenu = new JMenu();
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65 JMenuItem sequenceName = new JMenuItem();
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67 JMenuItem unGroupMenuItem = new JMenuItem();
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68 JMenuItem outline = new JMenuItem();
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69 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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70 JMenu colourMenu = new JMenu();
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71 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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72 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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73 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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74 JMenu editMenu = new JMenu();
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75 JMenuItem cut = new JMenuItem();
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76 JMenuItem copy = new JMenuItem();
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77 JMenuItem upperCase = new JMenuItem();
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78 JMenuItem lowerCase = new JMenuItem();
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79 JMenuItem toggle = new JMenuItem();
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80 JMenu pdbMenu = new JMenu();
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81 JMenuItem pdbFromFile = new JMenuItem();
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82 JMenuItem enterPDB = new JMenuItem();
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83 JMenuItem discoverPDB = new JMenuItem();
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84 JMenu outputMenu = new JMenu();
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85 JMenuItem sequenceFeature = new JMenuItem();
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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 int start = Math.max(sequence.getName().length()-15, 0);
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148 sequenceMenu.setText(sequence.getName().substring(start));
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150 JMenuItem menuItem;
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151 if( seq.getDatasetSequence().getPDBId() != null)
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153 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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156 while (e.hasMoreElements())
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158 final PDBEntry pdb = (PDBEntry) e.nextElement();
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160 menuItem = new JMenuItem();
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161 menuItem.setText("View PDB entry: " + pdb.getId());
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162 menuItem.addActionListener(new java.awt.event.ActionListener()
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164 public void actionPerformed(ActionEvent e)
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166 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
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169 sequenceMenu.add(menuItem);
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173 menuItem = new JMenuItem("Hide Sequences");
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174 menuItem.addActionListener(new java.awt.event.ActionListener()
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176 public void actionPerformed(ActionEvent e)
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178 hideSequences(false);
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183 if(ap.av.getSelectionGroup() !=null
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184 && ap.av.getSelectionGroup().getSize(false)>1)
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186 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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187 menuItem.addActionListener(new java.awt.event.ActionListener()
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189 public void actionPerformed(ActionEvent e)
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191 hideSequences(true);
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194 sequenceMenu.add(menuItem);
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197 if (ap.av.hasHiddenRows)
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199 final int index = ap.av.alignment.findIndex(seq);
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201 if (ap.av.adjustForHiddenSeqs(index) -
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202 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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204 menuItem = new JMenuItem("Reveal Sequences");
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205 menuItem.addActionListener(new ActionListener()
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207 public void actionPerformed(ActionEvent e)
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209 ap.av.showSequence(index);
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210 if (ap.overviewPanel != null)
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211 ap.overviewPanel.updateOverviewImage();
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217 menuItem = new JMenuItem("Reveal All");
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218 menuItem.addActionListener(new ActionListener()
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220 public void actionPerformed(ActionEvent e)
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222 ap.av.showAllHiddenSeqs();
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223 if (ap.overviewPanel != null)
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224 ap.overviewPanel.updateOverviewImage();
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236 SequenceGroup sg = ap.av.getSelectionGroup();
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240 groupName.setText(sg.getName());
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242 if (sg.cs instanceof ZappoColourScheme)
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244 zappoColour.setSelected(true);
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246 else if (sg.cs instanceof TaylorColourScheme)
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248 taylorColour.setSelected(true);
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250 else if (sg.cs instanceof PIDColourScheme)
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252 PIDColour.setSelected(true);
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254 else if (sg.cs instanceof Blosum62ColourScheme)
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256 BLOSUM62Colour.setSelected(true);
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258 else if (sg.cs instanceof UserColourScheme)
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260 userDefinedColour.setSelected(true);
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262 else if (sg.cs instanceof HydrophobicColourScheme)
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264 hydrophobicityColour.setSelected(true);
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266 else if (sg.cs instanceof HelixColourScheme)
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268 helixColour.setSelected(true);
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270 else if (sg.cs instanceof StrandColourScheme)
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272 strandColour.setSelected(true);
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274 else if (sg.cs instanceof TurnColourScheme)
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276 turnColour.setSelected(true);
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278 else if (sg.cs instanceof BuriedColourScheme)
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280 buriedColour.setSelected(true);
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282 else if (sg.cs instanceof ClustalxColourScheme)
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284 clustalColour.setSelected(true);
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288 noColourmenuItem.setSelected(true);
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291 if (sg.cs!=null && sg.cs.conservationApplied())
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293 conservationMenuItem.setSelected(true);
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296 showText.setSelected(sg.getDisplayText());
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297 showColourText.setSelected(sg.getColourText());
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298 showBoxes.setSelected(sg.getDisplayBoxes());
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302 groupMenu.setVisible(false);
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303 editMenu.setVisible(false);
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306 if (!ap.av.alignment.getGroups().contains(sg))
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308 unGroupMenuItem.setVisible(false);
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314 sequenceMenu.setVisible(false);
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315 pdbMenu.setVisible(false);
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318 if(links != null && links.size()>0)
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320 JMenu linkMenu = new JMenu("Link");
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322 for(int i=0; i<links.size(); i++)
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324 String link = links.elementAt(i).toString();
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325 final String label = link.substring(0, link.indexOf("|"));
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326 item = new JMenuItem(label);
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329 if (link.indexOf("$SEQUENCE_ID$") > -1)
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331 String id = seq.getName();
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332 if (id.indexOf("|") > -1)
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333 id = id.substring(id.lastIndexOf("|") + 1);
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335 url = link.substring(link.indexOf("|") + 1,
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336 link.indexOf("$SEQUENCE_ID$"))
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338 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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341 url = link.substring(link.lastIndexOf("|")+1);
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344 item.addActionListener(new java.awt.event.ActionListener()
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346 public void actionPerformed(ActionEvent e)
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352 linkMenu.add(item);
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355 sequenceMenu.add(linkMenu);
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365 * @throws Exception DOCUMENT ME!
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367 private void jbInit() throws Exception
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369 groupMenu.setText("Group");
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370 groupMenu.setText("Selection");
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371 groupName.setText("Name");
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372 groupName.addActionListener(new java.awt.event.ActionListener()
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374 public void actionPerformed(ActionEvent e)
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376 groupName_actionPerformed(e);
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379 sequenceMenu.setText("Sequence");
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380 sequenceName.setText("Edit Name/Description");
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381 sequenceName.addActionListener(new java.awt.event.ActionListener()
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383 public void actionPerformed(ActionEvent e)
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385 sequenceName_actionPerformed(e);
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388 PIDColour.setFocusPainted(false);
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389 unGroupMenuItem.setText("Remove Group");
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390 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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392 public void actionPerformed(ActionEvent e)
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394 unGroupMenuItem_actionPerformed(e);
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398 outline.setText("Border colour");
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399 outline.addActionListener(new java.awt.event.ActionListener()
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401 public void actionPerformed(ActionEvent e)
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403 outline_actionPerformed(e);
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406 nucleotideMenuItem.setText("Nucleotide");
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407 nucleotideMenuItem.addActionListener(new ActionListener()
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409 public void actionPerformed(ActionEvent e)
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411 nucleotideMenuItem_actionPerformed(e);
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414 colourMenu.setText("Group Colour");
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415 showBoxes.setText("Boxes");
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416 showBoxes.setState(true);
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417 showBoxes.addActionListener(new ActionListener()
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419 public void actionPerformed(ActionEvent e)
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421 showBoxes_actionPerformed(e);
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424 showText.setText("Text");
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425 showText.setState(true);
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426 showText.addActionListener(new ActionListener()
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428 public void actionPerformed(ActionEvent e)
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430 showText_actionPerformed(e);
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433 showColourText.setText("Colour Text");
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434 showColourText.addActionListener(new ActionListener()
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436 public void actionPerformed(ActionEvent e)
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438 showColourText_actionPerformed(e);
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441 editMenu.setText("Edit");
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442 cut.setText("Cut");
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443 cut.addActionListener(new ActionListener()
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445 public void actionPerformed(ActionEvent e)
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447 cut_actionPerformed(e);
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450 upperCase.setText("To Upper Case");
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451 upperCase.addActionListener(new ActionListener()
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453 public void actionPerformed(ActionEvent e)
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455 upperCase_actionPerformed(e);
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458 copy.setText("Copy");
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459 copy.addActionListener(new ActionListener()
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461 public void actionPerformed(ActionEvent e)
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463 copy_actionPerformed(e);
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466 lowerCase.setText("To Lower Case");
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467 lowerCase.addActionListener(new ActionListener()
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469 public void actionPerformed(ActionEvent e)
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471 lowerCase_actionPerformed(e);
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474 toggle.setText("Toggle Case");
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475 toggle.addActionListener(new ActionListener()
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477 public void actionPerformed(ActionEvent e)
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479 toggle_actionPerformed(e);
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482 pdbMenu.setText("Associate Structure with Sequence");
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483 pdbFromFile.setText("From File");
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484 pdbFromFile.addActionListener(new ActionListener()
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486 public void actionPerformed(ActionEvent e)
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488 pdbFromFile_actionPerformed(e);
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491 enterPDB.setText("Enter PDB Id");
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492 enterPDB.addActionListener(new ActionListener()
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494 public void actionPerformed(ActionEvent e)
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496 enterPDB_actionPerformed(e);
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499 discoverPDB.setText("Discover PDB ids");
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500 discoverPDB.addActionListener(new ActionListener()
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502 public void actionPerformed(ActionEvent e)
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504 discoverPDB_actionPerformed(e);
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507 outputMenu.setText("Output to Textbox...");
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508 sequenceFeature.setText("Create Sequence Feature");
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509 sequenceFeature.addActionListener(new ActionListener()
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511 public void actionPerformed(ActionEvent e)
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513 sequenceFeature_actionPerformed(e);
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519 groupMenu.add(editMenu);
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520 groupMenu.add(outputMenu);
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521 groupMenu.addSeparator();
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522 groupMenu.add(sequenceFeature);
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523 groupMenu.addSeparator();
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524 groupMenu.add(groupName);
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525 groupMenu.add(unGroupMenuItem);
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526 groupMenu.add(colourMenu);
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527 groupMenu.add(showBoxes);
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528 groupMenu.add(showText);
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529 groupMenu.add(showColourText);
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530 groupMenu.add(outline);
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531 sequenceMenu.add(sequenceName);
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532 sequenceMenu.add(pdbMenu);
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533 colourMenu.add(noColourmenuItem);
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534 colourMenu.add(clustalColour);
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535 colourMenu.add(BLOSUM62Colour);
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536 colourMenu.add(PIDColour);
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537 colourMenu.add(zappoColour);
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538 colourMenu.add(taylorColour);
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539 colourMenu.add(hydrophobicityColour);
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540 colourMenu.add(helixColour);
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541 colourMenu.add(strandColour);
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542 colourMenu.add(turnColour);
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543 colourMenu.add(buriedColour);
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544 colourMenu.add(nucleotideMenuItem);
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545 colourMenu.add(userDefinedColour);
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547 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
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549 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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550 getUserColourSchemes().keys();
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552 while (userColours.hasMoreElements())
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554 JMenuItem item = new JMenuItem(userColours.
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555 nextElement().toString());
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556 item.addActionListener(new ActionListener()
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558 public void actionPerformed(ActionEvent evt)
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560 userDefinedColour_actionPerformed(evt);
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563 colourMenu.add(item);
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568 colourMenu.addSeparator();
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569 colourMenu.add(abovePIDColour);
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570 colourMenu.add(conservationMenuItem);
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571 editMenu.add(copy);
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573 editMenu.add(upperCase);
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574 editMenu.add(lowerCase);
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575 editMenu.add(toggle);
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576 pdbMenu.add(pdbFromFile);
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577 pdbMenu.add(enterPDB);
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578 pdbMenu.add(discoverPDB);
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579 noColourmenuItem.setText("None");
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580 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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582 public void actionPerformed(ActionEvent e)
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584 noColourmenuItem_actionPerformed(e);
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588 clustalColour.setText("Clustalx colours");
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589 clustalColour.addActionListener(new java.awt.event.ActionListener()
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591 public void actionPerformed(ActionEvent e)
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593 clustalColour_actionPerformed(e);
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596 zappoColour.setText("Zappo");
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597 zappoColour.addActionListener(new java.awt.event.ActionListener()
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599 public void actionPerformed(ActionEvent e)
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601 zappoColour_actionPerformed(e);
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604 taylorColour.setText("Taylor");
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605 taylorColour.addActionListener(new java.awt.event.ActionListener()
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607 public void actionPerformed(ActionEvent e)
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609 taylorColour_actionPerformed(e);
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612 hydrophobicityColour.setText("Hydrophobicity");
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613 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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615 public void actionPerformed(ActionEvent e)
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617 hydrophobicityColour_actionPerformed(e);
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620 helixColour.setText("Helix propensity");
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621 helixColour.addActionListener(new java.awt.event.ActionListener()
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623 public void actionPerformed(ActionEvent e)
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625 helixColour_actionPerformed(e);
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628 strandColour.setText("Strand propensity");
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629 strandColour.addActionListener(new java.awt.event.ActionListener()
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631 public void actionPerformed(ActionEvent e)
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633 strandColour_actionPerformed(e);
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636 turnColour.setText("Turn propensity");
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637 turnColour.addActionListener(new java.awt.event.ActionListener()
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639 public void actionPerformed(ActionEvent e)
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641 turnColour_actionPerformed(e);
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644 buriedColour.setText("Buried Index");
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645 buriedColour.addActionListener(new java.awt.event.ActionListener()
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647 public void actionPerformed(ActionEvent e)
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649 buriedColour_actionPerformed(e);
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652 abovePIDColour.setText("Above % Identity");
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653 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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655 public void actionPerformed(ActionEvent e)
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657 abovePIDColour_actionPerformed(e);
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660 userDefinedColour.setText("User Defined...");
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661 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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663 public void actionPerformed(ActionEvent e)
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665 userDefinedColour_actionPerformed(e);
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668 PIDColour.setText("Percentage Identity");
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669 PIDColour.addActionListener(new java.awt.event.ActionListener()
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671 public void actionPerformed(ActionEvent e)
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673 PIDColour_actionPerformed(e);
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676 BLOSUM62Colour.setText("BLOSUM62");
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677 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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679 public void actionPerformed(ActionEvent e)
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681 BLOSUM62Colour_actionPerformed(e);
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684 conservationMenuItem.setText("Conservation");
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685 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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687 public void actionPerformed(ActionEvent e)
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689 conservationMenuItem_actionPerformed(e);
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699 if (ap.overviewPanel != null)
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700 ap.overviewPanel.updateOverviewImage();
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702 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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708 * @param e DOCUMENT ME!
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710 protected void clustalColour_actionPerformed(ActionEvent e)
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712 SequenceGroup sg = getGroup();
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713 sg.cs = new ClustalxColourScheme(sg.getSequences(true),
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714 ap.av.alignment.getWidth());
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721 * @param e DOCUMENT ME!
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723 protected void zappoColour_actionPerformed(ActionEvent e)
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725 getGroup().cs = new ZappoColourScheme();
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732 * @param e DOCUMENT ME!
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734 protected void taylorColour_actionPerformed(ActionEvent e)
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736 getGroup().cs = new TaylorColourScheme();
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743 * @param e DOCUMENT ME!
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745 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
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747 getGroup().cs = new HydrophobicColourScheme();
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754 * @param e DOCUMENT ME!
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756 protected void helixColour_actionPerformed(ActionEvent e)
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758 getGroup().cs = new HelixColourScheme();
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765 * @param e DOCUMENT ME!
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767 protected void strandColour_actionPerformed(ActionEvent e)
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769 getGroup().cs = new StrandColourScheme();
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776 * @param e DOCUMENT ME!
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778 protected void turnColour_actionPerformed(ActionEvent e)
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780 getGroup().cs = new TurnColourScheme();
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787 * @param e DOCUMENT ME!
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789 protected void buriedColour_actionPerformed(ActionEvent e)
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791 getGroup().cs = new BuriedColourScheme();
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798 * @param e DOCUMENT ME!
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800 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
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802 getGroup().cs = new NucleotideColourScheme();
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809 * @param e DOCUMENT ME!
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811 protected void abovePIDColour_actionPerformed(ActionEvent e)
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813 SequenceGroup sg = getGroup();
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817 if (abovePIDColour.isSelected())
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819 sg.cs.setConsensus(AAFrequency.calculate(
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820 sg.getSequences(true), 0,
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821 ap.av.alignment.getWidth()));
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823 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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824 getGroup().getName());
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826 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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828 SliderPanel.showPIDSlider();
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830 else // remove PIDColouring
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832 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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841 * @param e DOCUMENT ME!
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843 protected void userDefinedColour_actionPerformed(ActionEvent e)
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845 SequenceGroup sg = getGroup();
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847 if (e.getActionCommand().equals("User Defined..."))
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848 new UserDefinedColours(ap, sg);
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851 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
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852 getUserColourSchemes().get(e.getActionCommand());
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861 * @param e DOCUMENT ME!
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863 protected void PIDColour_actionPerformed(ActionEvent e)
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865 SequenceGroup sg = getGroup();
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866 sg.cs = new PIDColourScheme();
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867 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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868 ap.av.alignment.getWidth()));
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875 * @param e DOCUMENT ME!
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877 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
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879 SequenceGroup sg = getGroup();
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881 sg.cs = new Blosum62ColourScheme();
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883 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
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884 ap.av.alignment.getWidth()));
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892 * @param e DOCUMENT ME!
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894 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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896 getGroup().cs = null;
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903 * @param e DOCUMENT ME!
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905 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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907 SequenceGroup sg = getGroup();
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911 if (conservationMenuItem.isSelected())
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913 Conservation c = new Conservation("Group",
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914 ResidueProperties.propHash, 3,
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915 sg.getSequences(true), 0,
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916 ap.av.alignment.getWidth());
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919 c.verdict(false, ap.av.ConsPercGaps);
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921 sg.cs.setConservation(c);
\r
923 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
924 SliderPanel.showConservationSlider();
\r
926 else // remove ConservationColouring
\r
928 sg.cs.setConservation(null);
\r
937 * @param e DOCUMENT ME!
\r
939 protected void groupName_actionPerformed(ActionEvent e)
\r
941 SequenceGroup sg = getGroup();
\r
942 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
943 "Enter new group name", "Edit group name",
\r
944 JOptionPane.QUESTION_MESSAGE);
\r
952 groupName.setText(reply);
\r
958 * @param e DOCUMENT ME!
\r
960 protected void analyze_actionPerformed(ActionEvent e)
\r
962 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
963 JInternalFrame frame = new JInternalFrame();
\r
964 frame.setContentPane(cap);
\r
965 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
\r
967 SequenceGroup sg = getGroup();
\r
968 StringBuffer sb = new StringBuffer();
\r
970 for (int i = 0; i < sg.getSize(false); i++)
\r
972 Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
\r
973 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
\r
977 sb.append("Something amazing will happen soon");
\r
978 cap.setText(sb.toString());
\r
984 * @return DOCUMENT ME!
\r
986 SequenceGroup getGroup()
\r
988 SequenceGroup sg = ap.av.getSelectionGroup();
\r
989 // this method won't add a new group if it already exists
\r
991 ap.av.alignment.addGroup(sg);
\r
999 * @param e DOCUMENT ME!
\r
1001 void sequenceName_actionPerformed(ActionEvent e)
\r
1003 JLabel idlabel = new JLabel( " Sequence Name ");
\r
1004 JLabel desclabel = new JLabel("Sequence Description ");
\r
1005 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
1006 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
1007 JTextField id = new JTextField(sequence.getName(), 40);
\r
1008 JTextField description = new JTextField(sequence.getDescription(), 40);
\r
1009 JPanel panel = new JPanel(new BorderLayout());
\r
1010 JPanel panel2 = new JPanel(new BorderLayout());
\r
1011 panel2.add(idlabel, BorderLayout.WEST);
\r
1012 panel2.add(id, BorderLayout.CENTER);
\r
1013 panel.add(panel2, BorderLayout.NORTH);
\r
1014 panel2 = new JPanel(new BorderLayout());
\r
1015 panel2.add(desclabel, BorderLayout.WEST);
\r
1016 panel2.add(description, BorderLayout.CENTER);
\r
1017 panel.add(panel2, BorderLayout.SOUTH);
\r
1020 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
1021 panel, "Edit Sequence Name/Description",
\r
1022 JOptionPane.OK_CANCEL_OPTION );
\r
1025 if (reply != JOptionPane.OK_OPTION )
\r
1030 String s = id.getText();
\r
1034 if (s.indexOf(" ") > -1)
\r
1036 JOptionPane.showMessageDialog(ap,
\r
1037 "Spaces have been converted to \"_\"",
\r
1038 "No spaces allowed in Sequence Name",
\r
1039 JOptionPane.WARNING_MESSAGE);
\r
1042 s = s.replace(' ', '_');
\r
1043 sequence.getDatasetSequence().setName(s);
\r
1044 sequence.setName(s);
\r
1048 sequence.getDatasetSequence().setDescription(description.getText());
\r
1049 sequence.setDescription(description.getText());
\r
1055 * @param e DOCUMENT ME!
\r
1057 void unGroupMenuItem_actionPerformed(ActionEvent e)
\r
1059 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1060 ap.av.alignment.deleteGroup(sg);
\r
1061 ap.av.setSelectionGroup(null);
\r
1069 * @param e DOCUMENT ME!
\r
1071 protected void outline_actionPerformed(ActionEvent e)
\r
1073 SequenceGroup sg = getGroup();
\r
1074 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1079 sg.setOutlineColour(col);
\r
1088 * @param e DOCUMENT ME!
\r
1090 public void showBoxes_actionPerformed(ActionEvent e)
\r
1092 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1099 * @param e DOCUMENT ME!
\r
1101 public void showText_actionPerformed(ActionEvent e)
\r
1103 getGroup().setDisplayText(showText.isSelected());
\r
1110 * @param e DOCUMENT ME!
\r
1112 public void showColourText_actionPerformed(ActionEvent e)
\r
1114 getGroup().setColourText(showColourText.isSelected());
\r
1118 public void showLink(String url)
\r
1122 jalview.util.BrowserLauncher.openURL(url);
\r
1124 catch (Exception ex)
\r
1126 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1127 "Unixers: Couldn't find default web browser."
\r
1128 +"\nAdd the full path to your browser in Preferences.",
\r
1129 "Web browser not found", JOptionPane.WARNING_MESSAGE );
\r
1132 ex.printStackTrace();
\r
1136 void hideSequences(boolean representGroup)
\r
1138 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1139 if(sg==null || sg.getSize(false)<1)
\r
1141 ap.av.hideSequence(new SequenceI[]{sequence});
\r
1145 int gsize = sg.getSize(false);
\r
1146 SequenceI [] hseqs;
\r
1148 hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
\r
1151 for(int i=0; i<gsize; i++)
\r
1153 if(representGroup && sg.getSequenceAt(i)!=sequence)
\r
1155 sequence.addHiddenSequence(sg.getSequenceAt(i));
\r
1156 hseqs[index++] = sg.getSequenceAt(i);
\r
1158 else if(!representGroup)
\r
1160 hseqs[index++] = sg.getSequenceAt(i);
\r
1164 ap.av.hideSequence(hseqs);
\r
1166 ap.av.setSelectionGroup(null);
\r
1169 public void copy_actionPerformed(ActionEvent e)
\r
1171 ap.alignFrame.copy_actionPerformed(null);
\r
1174 public void cut_actionPerformed(ActionEvent e)
\r
1176 ap.alignFrame.cut_actionPerformed(null);
\r
1179 public void upperCase_actionPerformed(ActionEvent e)
\r
1181 changeCase(e.getSource());
\r
1184 public void lowerCase_actionPerformed(ActionEvent e)
\r
1186 changeCase(e.getSource());
\r
1189 public void toggle_actionPerformed(ActionEvent e)
\r
1191 changeCase(e.getSource());
\r
1194 void changeCase(Object source)
\r
1196 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1199 for (int g = 0; g < sg.getSize(true); g++)
\r
1201 int start = sg.getStartRes();
\r
1202 int end = sg.getEndRes() + 1;
\r
1206 if (ap.av.hasHiddenColumns)
\r
1208 end = ap.av.colSel.getHiddenBoundaryRight(start);
\r
1210 end = sg.getEndRes() + 1;
\r
1211 if (end > sg.getEndRes())
\r
1212 end = sg.getEndRes() + 1;
\r
1215 if (source == toggle)
\r
1216 ( (SequenceI) sg.getSequences(true).elementAt(g))
\r
1217 .toggleCase(start, end);
\r
1219 ( (SequenceI) sg.getSequences(true).elementAt(g))
\r
1220 .changeCase(source == upperCase, start, end);
\r
1222 if (ap.av.hasHiddenColumns)
\r
1224 start = ap.av.colSel.adjustForHiddenColumns(end);
\r
1225 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
\r
1229 while (end < sg.getEndRes());
\r
1231 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
\r
1235 public void outputText_actionPerformed(ActionEvent e)
\r
1237 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1238 Desktop.addInternalFrame(cap,
\r
1239 "Alignment output - " + e.getActionCommand(), 600,
\r
1242 String [] omitHidden = null;
\r
1244 if(ap.av.hasHiddenColumns)
\r
1246 System.out.println("PROMPT USER HERE");
\r
1247 omitHidden = ap.av.getViewAsString(true);
\r
1250 cap.setText(new FormatAdapter().formatSequences(
\r
1251 e.getActionCommand(),
\r
1252 ap.av.getSelectionAsNewSequence(),
\r
1257 public void pdbFromFile_actionPerformed(ActionEvent e)
\r
1259 jalview.io.JalviewFileChooser chooser
\r
1260 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1262 "LAST_DIRECTORY"));
\r
1263 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1264 chooser.setDialogTitle("Select a PDB file");
\r
1265 chooser.setToolTipText("Load a PDB file");
\r
1267 int value = chooser.showOpenDialog(null);
\r
1269 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1271 PDBEntry entry = new PDBEntry();
\r
1272 String choice = chooser.getSelectedFile().getPath();
\r
1273 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1276 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1277 jalview.io.AppletFormatAdapter.FILE);
\r
1279 if (pdbfile.id == null)
\r
1281 String reply = JOptionPane.showInternalInputDialog(
\r
1283 "Couldn't find a PDB id in the file supplied."
\r
1284 + "Please enter an Id to identify this structure.",
\r
1285 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1286 if (reply == null)
\r
1289 entry.setId(reply);
\r
1292 entry.setId(pdbfile.id);
\r
1294 catch (java.io.IOException ex)
\r
1296 ex.printStackTrace();
\r
1299 entry.setFile(choice);
\r
1300 sequence.getDatasetSequence().addPDBId(entry);
\r
1305 public void enterPDB_actionPerformed(ActionEvent e)
\r
1307 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1308 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1310 if (id != null && id.length() > 0)
\r
1312 PDBEntry entry = new PDBEntry();
\r
1314 sequence.getDatasetSequence()
\r
1319 public void discoverPDB_actionPerformed(ActionEvent e)
\r
1321 new jalview.io.DBRefFetcher(
\r
1322 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r
1325 public void sequenceFeature_actionPerformed(ActionEvent e)
\r
1327 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1331 int gSize= sg.getSize(false);
\r
1332 SequenceI [] seqs = new SequenceI[gSize];
\r
1333 SequenceFeature [] features = new SequenceFeature[gSize];
\r
1335 for (int i = 0; i < gSize; i++)
\r
1337 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1338 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1339 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1340 features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
\r
1343 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1344 .createNewFeatures(seqs, features))
\r
1346 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1347 ap.av.setShowSequenceFeatures(true);
\r
1348 ap.highlightSearchResults(null);
\r