2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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24 import java.awt.event.*;
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25 import javax.swing.*;
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28 import jalview.analysis.*;
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29 import jalview.commands.*;
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30 import jalview.datamodel.*;
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31 import jalview.io.*;
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32 import jalview.schemes.*;
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38 * @version $Revision$
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40 public class PopupMenu
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43 JMenu groupMenu = new JMenu();
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44 JMenuItem groupName = new JMenuItem();
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45 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
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46 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
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47 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
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48 protected JRadioButtonMenuItem hydrophobicityColour = new
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49 JRadioButtonMenuItem();
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50 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
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51 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
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52 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
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53 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
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54 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
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55 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
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56 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
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57 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
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58 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
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59 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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61 JMenu sequenceMenu = new JMenu();
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62 JMenuItem sequenceName = new JMenuItem();
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64 JMenuItem unGroupMenuItem = new JMenuItem();
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65 JMenuItem outline = new JMenuItem();
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66 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
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67 JMenu colourMenu = new JMenu();
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68 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
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69 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
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70 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
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71 JMenu editMenu = new JMenu();
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72 JMenuItem cut = new JMenuItem();
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73 JMenuItem copy = new JMenuItem();
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74 JMenuItem upperCase = new JMenuItem();
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75 JMenuItem lowerCase = new JMenuItem();
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76 JMenuItem toggle = new JMenuItem();
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77 JMenu pdbMenu = new JMenu();
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78 JMenuItem pdbFromFile = new JMenuItem();
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79 JMenuItem enterPDB = new JMenuItem();
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80 JMenuItem discoverPDB = new JMenuItem();
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81 JMenu outputMenu = new JMenu();
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82 JMenuItem sequenceFeature = new JMenuItem();
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83 JMenuItem textColour = new JMenuItem();
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84 JMenu jMenu1 = new JMenu();
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85 JMenu structureMenu = new JMenu();
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86 JMenu viewStructureMenu = new JMenu();
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87 JMenu colStructureMenu = new JMenu();
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88 JMenuItem editSequence = new JMenuItem();
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91 * Creates a new PopupMenu object.
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93 * @param ap DOCUMENT ME!
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94 * @param seq DOCUMENT ME!
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96 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
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98 ///////////////////////////////////////////////////////////
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99 // If this is activated from the sequence panel, the user may want to
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100 // edit or annotate a particular residue. Therefore display the residue menu
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102 // If from the IDPanel, we must display the sequence menu
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103 //////////////////////////////////////////////////////////
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107 ButtonGroup colours = new ButtonGroup();
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108 colours.add(noColourmenuItem);
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109 colours.add(clustalColour);
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110 colours.add(zappoColour);
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111 colours.add(taylorColour);
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112 colours.add(hydrophobicityColour);
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113 colours.add(helixColour);
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114 colours.add(strandColour);
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115 colours.add(turnColour);
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116 colours.add(buriedColour);
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117 colours.add(abovePIDColour);
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118 colours.add(userDefinedColour);
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119 colours.add(PIDColour);
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120 colours.add(BLOSUM62Colour);
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122 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
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124 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
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127 item.addActionListener(new java.awt.event.ActionListener()
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129 public void actionPerformed(ActionEvent e)
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131 outputText_actionPerformed(e);
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135 outputMenu.add(item);
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142 catch (Exception e)
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144 e.printStackTrace();
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149 sequenceMenu.setText(sequence.getName());
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151 JMenuItem menuItem;
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152 if (seq.getDatasetSequence().getPDBId() != null)
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154 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
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157 while (e.hasMoreElements())
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159 final PDBEntry pdb = (PDBEntry) e.nextElement();
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161 menuItem = new JMenuItem();
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162 menuItem.setText(pdb.getId());
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163 menuItem.addActionListener(new java.awt.event.ActionListener()
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165 public void actionPerformed(ActionEvent e)
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167 Vector seqs = new Vector();
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168 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
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170 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
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174 for(int p=0; p<pdbs.size(); p++)
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176 PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
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177 if(p1.getId().equals(pdb.getId()))
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179 if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
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180 seqs.addElement(ap.av.alignment.getSequenceAt(i));
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187 SequenceI [] seqs2 = new SequenceI[seqs.size()];
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188 seqs.toArray(seqs2);
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190 new AppJMol(pdb, seqs2, ap);
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193 viewStructureMenu.add(menuItem);
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195 menuItem = new JMenuItem();
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196 menuItem.setText(pdb.getId());
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197 menuItem.addActionListener(new java.awt.event.ActionListener()
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199 public void actionPerformed(ActionEvent e)
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201 colourByStructure(pdb.getId());
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204 colStructureMenu.add(menuItem);
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208 menuItem = new JMenuItem("Hide Sequences");
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209 menuItem.addActionListener(new java.awt.event.ActionListener()
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211 public void actionPerformed(ActionEvent e)
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213 hideSequences(false);
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218 if (ap.av.getSelectionGroup() != null
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219 && ap.av.getSelectionGroup().getSize() > 1)
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221 menuItem = new JMenuItem("Represent Group with " + seq.getName());
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222 menuItem.addActionListener(new java.awt.event.ActionListener()
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224 public void actionPerformed(ActionEvent e)
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226 hideSequences(true);
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229 sequenceMenu.add(menuItem);
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232 if (ap.av.hasHiddenRows)
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234 final int index = ap.av.alignment.findIndex(seq);
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236 if (ap.av.adjustForHiddenSeqs(index) -
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237 ap.av.adjustForHiddenSeqs(index - 1) > 1)
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239 menuItem = new JMenuItem("Reveal Sequences");
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240 menuItem.addActionListener(new ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 ap.av.showSequence(index);
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245 if (ap.overviewPanel != null)
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247 ap.overviewPanel.updateOverviewImage();
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254 menuItem = new JMenuItem("Reveal All");
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255 menuItem.addActionListener(new ActionListener()
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257 public void actionPerformed(ActionEvent e)
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259 ap.av.showAllHiddenSeqs();
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260 if (ap.overviewPanel != null)
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262 ap.overviewPanel.updateOverviewImage();
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272 SequenceGroup sg = ap.av.getSelectionGroup();
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276 groupName.setText(sg.getName());
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278 if (sg.cs instanceof ZappoColourScheme)
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280 zappoColour.setSelected(true);
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282 else if (sg.cs instanceof TaylorColourScheme)
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284 taylorColour.setSelected(true);
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286 else if (sg.cs instanceof PIDColourScheme)
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288 PIDColour.setSelected(true);
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290 else if (sg.cs instanceof Blosum62ColourScheme)
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292 BLOSUM62Colour.setSelected(true);
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294 else if (sg.cs instanceof UserColourScheme)
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296 userDefinedColour.setSelected(true);
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298 else if (sg.cs instanceof HydrophobicColourScheme)
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300 hydrophobicityColour.setSelected(true);
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302 else if (sg.cs instanceof HelixColourScheme)
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304 helixColour.setSelected(true);
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306 else if (sg.cs instanceof StrandColourScheme)
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308 strandColour.setSelected(true);
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310 else if (sg.cs instanceof TurnColourScheme)
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312 turnColour.setSelected(true);
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314 else if (sg.cs instanceof BuriedColourScheme)
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316 buriedColour.setSelected(true);
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318 else if (sg.cs instanceof ClustalxColourScheme)
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320 clustalColour.setSelected(true);
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324 noColourmenuItem.setSelected(true);
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327 if (sg.cs != null && sg.cs.conservationApplied())
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329 conservationMenuItem.setSelected(true);
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332 showText.setSelected(sg.getDisplayText());
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333 showColourText.setSelected(sg.getColourText());
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334 showBoxes.setSelected(sg.getDisplayBoxes());
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338 groupMenu.setVisible(false);
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339 editMenu.setVisible(false);
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342 if (!ap.av.alignment.getGroups().contains(sg))
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344 unGroupMenuItem.setVisible(false);
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349 sequenceMenu.setVisible(false);
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350 structureMenu.setVisible(false);
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353 if (links != null && links.size() > 0)
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355 JMenu linkMenu = new JMenu("Link");
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357 for (int i = 0; i < links.size(); i++)
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359 String link = links.elementAt(i).toString();
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360 final String label = link.substring(0, link.indexOf("|"));
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361 item = new JMenuItem(label);
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364 if (link.indexOf("$SEQUENCE_ID$") > -1)
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366 String id = seq.getName();
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367 if (id.indexOf("|") > -1)
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369 id = id.substring(id.lastIndexOf("|") + 1);
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372 url = link.substring(link.indexOf("|") + 1,
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373 link.indexOf("$SEQUENCE_ID$"))
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375 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
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379 url = link.substring(link.lastIndexOf("|") + 1);
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382 item.addActionListener(new java.awt.event.ActionListener()
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384 public void actionPerformed(ActionEvent e)
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390 linkMenu.add(item);
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392 if (sequence != null)
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394 sequenceMenu.add(linkMenu);
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406 * @throws Exception DOCUMENT ME!
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408 private void jbInit()
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411 groupMenu.setText("Group");
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412 groupMenu.setText("Selection");
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413 groupName.setText("Name");
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414 groupName.addActionListener(new java.awt.event.ActionListener()
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416 public void actionPerformed(ActionEvent e)
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418 groupName_actionPerformed();
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421 sequenceMenu.setText("Sequence");
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422 sequenceName.setText("Edit Name/Description");
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423 sequenceName.addActionListener(new java.awt.event.ActionListener()
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425 public void actionPerformed(ActionEvent e)
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427 sequenceName_actionPerformed();
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430 PIDColour.setFocusPainted(false);
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431 unGroupMenuItem.setText("Remove Group");
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432 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
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434 public void actionPerformed(ActionEvent e)
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436 unGroupMenuItem_actionPerformed();
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440 outline.setText("Border colour");
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441 outline.addActionListener(new java.awt.event.ActionListener()
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443 public void actionPerformed(ActionEvent e)
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445 outline_actionPerformed();
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448 nucleotideMenuItem.setText("Nucleotide");
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449 nucleotideMenuItem.addActionListener(new ActionListener()
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451 public void actionPerformed(ActionEvent e)
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453 nucleotideMenuItem_actionPerformed();
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456 colourMenu.setText("Group Colour");
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457 showBoxes.setText("Boxes");
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458 showBoxes.setState(true);
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459 showBoxes.addActionListener(new ActionListener()
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461 public void actionPerformed(ActionEvent e)
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463 showBoxes_actionPerformed();
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466 showText.setText("Text");
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467 showText.setState(true);
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468 showText.addActionListener(new ActionListener()
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470 public void actionPerformed(ActionEvent e)
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472 showText_actionPerformed();
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475 showColourText.setText("Colour Text");
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476 showColourText.addActionListener(new ActionListener()
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478 public void actionPerformed(ActionEvent e)
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480 showColourText_actionPerformed();
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483 editMenu.setText("Edit");
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484 cut.setText("Cut");
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485 cut.addActionListener(new ActionListener()
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487 public void actionPerformed(ActionEvent e)
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489 cut_actionPerformed();
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492 upperCase.setText("To Upper Case");
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493 upperCase.addActionListener(new ActionListener()
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495 public void actionPerformed(ActionEvent e)
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500 copy.setText("Copy");
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501 copy.addActionListener(new ActionListener()
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503 public void actionPerformed(ActionEvent e)
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505 copy_actionPerformed();
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508 lowerCase.setText("To Lower Case");
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509 lowerCase.addActionListener(new ActionListener()
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511 public void actionPerformed(ActionEvent e)
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516 toggle.setText("Toggle Case");
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517 toggle.addActionListener(new ActionListener()
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519 public void actionPerformed(ActionEvent e)
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524 pdbMenu.setText("Associate Structure with Sequence");
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525 pdbFromFile.setText("From File");
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526 pdbFromFile.addActionListener(new ActionListener()
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528 public void actionPerformed(ActionEvent e)
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530 pdbFromFile_actionPerformed();
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533 enterPDB.setText("Enter PDB Id");
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534 enterPDB.addActionListener(new ActionListener()
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536 public void actionPerformed(ActionEvent e)
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538 enterPDB_actionPerformed();
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541 discoverPDB.setText("Discover PDB ids");
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542 discoverPDB.addActionListener(new ActionListener()
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544 public void actionPerformed(ActionEvent e)
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546 discoverPDB_actionPerformed();
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549 outputMenu.setText("Output to Textbox...");
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550 sequenceFeature.setText("Create Sequence Feature");
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551 sequenceFeature.addActionListener(new ActionListener()
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553 public void actionPerformed(ActionEvent e)
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555 sequenceFeature_actionPerformed();
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558 textColour.setText("Text Colour");
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559 textColour.addActionListener(new ActionListener()
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561 public void actionPerformed(ActionEvent e)
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563 textColour_actionPerformed();
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566 jMenu1.setText("Group");
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567 structureMenu.setText("Structure");
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568 viewStructureMenu.setText("View Structure");
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569 colStructureMenu.setText("Colour By Structure");
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570 editSequence.setText("Edit Sequence...");
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571 editSequence.addActionListener(new ActionListener()
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573 public void actionPerformed(ActionEvent actionEvent)
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575 editSequence_actionPerformed(actionEvent);
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582 this.add(structureMenu);
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583 groupMenu.add(editMenu);
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584 groupMenu.add(outputMenu);
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585 groupMenu.add(sequenceFeature);
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586 groupMenu.add(jMenu1);
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587 sequenceMenu.add(sequenceName);
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588 colourMenu.add(textColour);
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589 colourMenu.add(noColourmenuItem);
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590 colourMenu.add(clustalColour);
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591 colourMenu.add(BLOSUM62Colour);
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592 colourMenu.add(PIDColour);
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593 colourMenu.add(zappoColour);
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594 colourMenu.add(taylorColour);
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595 colourMenu.add(hydrophobicityColour);
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596 colourMenu.add(helixColour);
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597 colourMenu.add(strandColour);
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598 colourMenu.add(turnColour);
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599 colourMenu.add(buriedColour);
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600 colourMenu.add(nucleotideMenuItem);
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601 colourMenu.add(userDefinedColour);
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603 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
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605 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
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606 getUserColourSchemes().keys();
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608 while (userColours.hasMoreElements())
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610 JMenuItem item = new JMenuItem(userColours.
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611 nextElement().toString());
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612 item.addActionListener(new ActionListener()
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614 public void actionPerformed(ActionEvent evt)
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616 userDefinedColour_actionPerformed(evt);
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619 colourMenu.add(item);
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623 colourMenu.addSeparator();
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624 colourMenu.add(abovePIDColour);
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625 colourMenu.add(conservationMenuItem);
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626 editMenu.add(copy);
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628 editMenu.add(editSequence);
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629 editMenu.add(upperCase);
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630 editMenu.add(lowerCase);
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631 editMenu.add(toggle);
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632 pdbMenu.add(pdbFromFile);
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633 pdbMenu.add(enterPDB);
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634 pdbMenu.add(discoverPDB);
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635 jMenu1.add(groupName);
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636 jMenu1.add(unGroupMenuItem);
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637 jMenu1.add(colourMenu);
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638 jMenu1.add(showBoxes);
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639 jMenu1.add(showText);
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640 jMenu1.add(showColourText);
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641 jMenu1.add(outline);
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642 structureMenu.add(pdbMenu);
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643 structureMenu.add(viewStructureMenu);
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644 structureMenu.add(colStructureMenu);
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645 noColourmenuItem.setText("None");
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646 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
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648 public void actionPerformed(ActionEvent e)
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650 noColourmenuItem_actionPerformed();
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654 clustalColour.setText("Clustalx colours");
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655 clustalColour.addActionListener(new java.awt.event.ActionListener()
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657 public void actionPerformed(ActionEvent e)
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659 clustalColour_actionPerformed();
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662 zappoColour.setText("Zappo");
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663 zappoColour.addActionListener(new java.awt.event.ActionListener()
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665 public void actionPerformed(ActionEvent e)
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667 zappoColour_actionPerformed();
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670 taylorColour.setText("Taylor");
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671 taylorColour.addActionListener(new java.awt.event.ActionListener()
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673 public void actionPerformed(ActionEvent e)
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675 taylorColour_actionPerformed();
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678 hydrophobicityColour.setText("Hydrophobicity");
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679 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
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681 public void actionPerformed(ActionEvent e)
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683 hydrophobicityColour_actionPerformed();
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686 helixColour.setText("Helix propensity");
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687 helixColour.addActionListener(new java.awt.event.ActionListener()
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689 public void actionPerformed(ActionEvent e)
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691 helixColour_actionPerformed();
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694 strandColour.setText("Strand propensity");
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695 strandColour.addActionListener(new java.awt.event.ActionListener()
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697 public void actionPerformed(ActionEvent e)
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699 strandColour_actionPerformed();
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702 turnColour.setText("Turn propensity");
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703 turnColour.addActionListener(new java.awt.event.ActionListener()
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705 public void actionPerformed(ActionEvent e)
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707 turnColour_actionPerformed();
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710 buriedColour.setText("Buried Index");
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711 buriedColour.addActionListener(new java.awt.event.ActionListener()
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713 public void actionPerformed(ActionEvent e)
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715 buriedColour_actionPerformed();
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718 abovePIDColour.setText("Above % Identity");
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719 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
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721 public void actionPerformed(ActionEvent e)
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723 abovePIDColour_actionPerformed();
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726 userDefinedColour.setText("User Defined...");
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727 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
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729 public void actionPerformed(ActionEvent e)
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731 userDefinedColour_actionPerformed(e);
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734 PIDColour.setText("Percentage Identity");
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735 PIDColour.addActionListener(new java.awt.event.ActionListener()
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737 public void actionPerformed(ActionEvent e)
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739 PIDColour_actionPerformed();
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742 BLOSUM62Colour.setText("BLOSUM62");
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743 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
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745 public void actionPerformed(ActionEvent e)
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747 BLOSUM62Colour_actionPerformed();
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750 conservationMenuItem.setText("Conservation");
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751 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
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753 public void actionPerformed(ActionEvent e)
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755 conservationMenuItem_actionPerformed();
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765 ap.paintAlignment(true);
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767 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
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773 * @param e DOCUMENT ME!
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775 protected void clustalColour_actionPerformed()
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777 SequenceGroup sg = getGroup();
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778 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
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779 ap.av.alignment.getWidth());
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786 * @param e DOCUMENT ME!
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788 protected void zappoColour_actionPerformed()
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790 getGroup().cs = new ZappoColourScheme();
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797 * @param e DOCUMENT ME!
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799 protected void taylorColour_actionPerformed()
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801 getGroup().cs = new TaylorColourScheme();
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808 * @param e DOCUMENT ME!
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810 protected void hydrophobicityColour_actionPerformed()
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812 getGroup().cs = new HydrophobicColourScheme();
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819 * @param e DOCUMENT ME!
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821 protected void helixColour_actionPerformed()
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823 getGroup().cs = new HelixColourScheme();
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830 * @param e DOCUMENT ME!
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832 protected void strandColour_actionPerformed()
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834 getGroup().cs = new StrandColourScheme();
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841 * @param e DOCUMENT ME!
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843 protected void turnColour_actionPerformed()
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845 getGroup().cs = new TurnColourScheme();
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852 * @param e DOCUMENT ME!
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854 protected void buriedColour_actionPerformed()
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856 getGroup().cs = new BuriedColourScheme();
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863 * @param e DOCUMENT ME!
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865 public void nucleotideMenuItem_actionPerformed()
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867 getGroup().cs = new NucleotideColourScheme();
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874 * @param e DOCUMENT ME!
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876 protected void abovePIDColour_actionPerformed()
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878 SequenceGroup sg = getGroup();
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884 if (abovePIDColour.isSelected())
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886 sg.cs.setConsensus(AAFrequency.calculate(
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887 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
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888 sg.getEndRes() + 1));
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890 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
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891 getGroup().getName());
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893 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
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895 SliderPanel.showPIDSlider();
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897 else // remove PIDColouring
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899 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
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908 * @param e DOCUMENT ME!
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910 protected void userDefinedColour_actionPerformed(ActionEvent e)
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912 SequenceGroup sg = getGroup();
\r
914 if (e.getActionCommand().equals("User Defined..."))
\r
916 new UserDefinedColours(ap, sg);
\r
920 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
921 getUserColourSchemes().get(e.getActionCommand());
\r
931 * @param e DOCUMENT ME!
\r
933 protected void PIDColour_actionPerformed()
\r
935 SequenceGroup sg = getGroup();
\r
936 sg.cs = new PIDColourScheme();
\r
937 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
938 hiddenRepSequences),
\r
940 sg.getEndRes() + 1));
\r
947 * @param e DOCUMENT ME!
\r
949 protected void BLOSUM62Colour_actionPerformed()
\r
951 SequenceGroup sg = getGroup();
\r
953 sg.cs = new Blosum62ColourScheme();
\r
955 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
956 hiddenRepSequences),
\r
958 sg.getEndRes() + 1));
\r
966 * @param e DOCUMENT ME!
\r
968 protected void noColourmenuItem_actionPerformed()
\r
970 getGroup().cs = null;
\r
977 * @param e DOCUMENT ME!
\r
979 protected void conservationMenuItem_actionPerformed()
\r
981 SequenceGroup sg = getGroup();
\r
987 if (conservationMenuItem.isSelected())
\r
989 Conservation c = new Conservation("Group",
\r
990 ResidueProperties.propHash, 3,
\r
991 sg.getSequences(ap.av.
\r
992 hiddenRepSequences),
\r
994 sg.getEndRes() + 1);
\r
997 c.verdict(false, ap.av.ConsPercGaps);
\r
999 sg.cs.setConservation(c);
\r
1001 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
1002 SliderPanel.showConservationSlider();
\r
1004 else // remove ConservationColouring
\r
1006 sg.cs.setConservation(null);
\r
1015 * @param e DOCUMENT ME!
\r
1017 protected void groupName_actionPerformed()
\r
1020 SequenceGroup sg = getGroup();
\r
1021 EditNameDialog dialog = new EditNameDialog(sg.getName(),
\r
1022 sg.getDescription(),
\r
1024 "Group Description ",
\r
1025 "Edit Group Name/Description");
\r
1027 if (!dialog.accept)
\r
1032 sg.setName(dialog.getName());
\r
1033 sg.setDescription(dialog.getDescription());
\r
1039 * @return DOCUMENT ME!
\r
1041 SequenceGroup getGroup()
\r
1043 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1044 // this method won't add a new group if it already exists
\r
1047 ap.av.alignment.addGroup(sg);
\r
1056 * @param e DOCUMENT ME!
\r
1058 void sequenceName_actionPerformed()
\r
1060 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
\r
1061 sequence.getDescription(),
\r
1062 " Sequence Name ",
\r
1063 "Sequence Description ",
\r
1064 "Edit Sequence Name/Description");
\r
1066 if (!dialog.accept)
\r
1071 if (dialog.getName() != null)
\r
1073 if (dialog.getName().indexOf(" ") > -1)
\r
1075 JOptionPane.showMessageDialog(ap,
\r
1076 "Spaces have been converted to \"_\"",
\r
1077 "No spaces allowed in Sequence Name",
\r
1078 JOptionPane.WARNING_MESSAGE);
\r
1081 sequence.setName(dialog.getName().replace(' ', '_'));
\r
1082 ap.paintAlignment(false);
\r
1085 sequence.setDescription(dialog.getDescription());
\r
1087 ap.av.firePropertyChange("alignment", null,
\r
1088 ap.av.getAlignment().getSequences());
\r
1095 * @param e DOCUMENT ME!
\r
1097 void unGroupMenuItem_actionPerformed()
\r
1099 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1100 ap.av.alignment.deleteGroup(sg);
\r
1101 ap.av.setSelectionGroup(null);
\r
1108 * @param e DOCUMENT ME!
\r
1110 protected void outline_actionPerformed()
\r
1112 SequenceGroup sg = getGroup();
\r
1113 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1118 sg.setOutlineColour(col);
\r
1127 * @param e DOCUMENT ME!
\r
1129 public void showBoxes_actionPerformed()
\r
1131 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1138 * @param e DOCUMENT ME!
\r
1140 public void showText_actionPerformed()
\r
1142 getGroup().setDisplayText(showText.isSelected());
\r
1149 * @param e DOCUMENT ME!
\r
1151 public void showColourText_actionPerformed()
\r
1153 getGroup().setColourText(showColourText.isSelected());
\r
1157 public void showLink(String url)
\r
1161 jalview.util.BrowserLauncher.openURL(url);
\r
1163 catch (Exception ex)
\r
1165 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1166 "Unixers: Couldn't find default web browser."
\r
1168 "\nAdd the full path to your browser in Preferences.",
\r
1169 "Web browser not found",
\r
1170 JOptionPane.WARNING_MESSAGE);
\r
1172 ex.printStackTrace();
\r
1176 void hideSequences(boolean representGroup)
\r
1178 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1179 if (sg == null || sg.getSize() < 1)
\r
1181 ap.av.hideSequence(new SequenceI[]
\r
1186 ap.av.setSelectionGroup(null);
\r
1188 if (representGroup)
\r
1190 ap.av.hideRepSequences(sequence, sg);
\r
1195 int gsize = sg.getSize();
\r
1196 SequenceI[] hseqs;
\r
1198 hseqs = new SequenceI[gsize];
\r
1201 for (int i = 0; i < gsize; i++)
\r
1203 hseqs[index++] = sg.getSequenceAt(i);
\r
1206 ap.av.hideSequence(hseqs);
\r
1209 public void copy_actionPerformed()
\r
1211 ap.alignFrame.copy_actionPerformed(null);
\r
1214 public void cut_actionPerformed()
\r
1216 ap.alignFrame.cut_actionPerformed(null);
\r
1219 void changeCase(ActionEvent e)
\r
1221 Object source = e.getSource();
\r
1222 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1226 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
\r
1227 sg.getStartRes(), sg.getEndRes() + 1);
\r
1229 String description;
\r
1232 if (source == toggle)
\r
1234 description = "Toggle Case";
\r
1235 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1237 else if (source == upperCase)
\r
1239 description = "To Upper Case";
\r
1240 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1244 description = "To Lower Case";
\r
1245 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1248 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1249 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1250 startEnd, caseChange
\r
1253 ap.alignFrame.addHistoryItem(caseCommand);
\r
1255 ap.av.firePropertyChange("alignment", null,
\r
1256 ap.av.getAlignment().getSequences());
\r
1261 public void outputText_actionPerformed(ActionEvent e)
\r
1263 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1264 cap.setForInput(null);
\r
1265 Desktop.addInternalFrame(cap,
\r
1266 "Alignment output - " + e.getActionCommand(), 600,
\r
1269 String[] omitHidden = null;
\r
1271 if (ap.av.hasHiddenColumns)
\r
1273 System.out.println("PROMPT USER HERE");
\r
1274 omitHidden = ap.av.getViewAsString(true);
\r
1277 cap.setText(new FormatAdapter().formatSequences(
\r
1278 e.getActionCommand(),
\r
1279 ap.av.getSelectionAsNewSequence(),
\r
1283 public void pdbFromFile_actionPerformed()
\r
1285 jalview.io.JalviewFileChooser chooser
\r
1286 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1288 "LAST_DIRECTORY"));
\r
1289 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1290 chooser.setDialogTitle("Select a PDB file");
\r
1291 chooser.setToolTipText("Load a PDB file");
\r
1293 int value = chooser.showOpenDialog(null);
\r
1295 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1297 PDBEntry entry = new PDBEntry();
\r
1298 String choice = chooser.getSelectedFile().getPath();
\r
1299 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1302 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1303 jalview.io.AppletFormatAdapter.FILE);
\r
1305 if (pdbfile.id == null)
\r
1307 String reply = JOptionPane.showInternalInputDialog(
\r
1309 "Couldn't find a PDB id in the file supplied."
\r
1310 + "Please enter an Id to identify this structure.",
\r
1311 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1312 if (reply == null)
\r
1317 entry.setId(reply);
\r
1321 entry.setId(pdbfile.id);
\r
1324 catch (java.io.IOException ex)
\r
1326 ex.printStackTrace();
\r
1329 entry.setFile(choice);
\r
1330 sequence.getDatasetSequence().addPDBId(entry);
\r
1335 public void enterPDB_actionPerformed()
\r
1337 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1338 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1340 if (id != null && id.length() > 0)
\r
1342 PDBEntry entry = new PDBEntry();
\r
1344 sequence.getDatasetSequence()
\r
1349 public void discoverPDB_actionPerformed()
\r
1351 SequenceI[] sequences =
\r
1352 ap.av.selectionGroup == null ?
\r
1353 new Sequence[]{sequence}
\r
1354 : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
\r
1356 new jalview.io.DBRefFetcher(sequences,
\r
1357 ap.alignFrame).fetchDBRefs(false);
\r
1360 public void sequenceFeature_actionPerformed()
\r
1362 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1368 int gSize = sg.getSize();
\r
1369 SequenceI[] seqs = new SequenceI[gSize];
\r
1370 SequenceFeature[] features = new SequenceFeature[gSize];
\r
1372 for (int i = 0; i < gSize; i++)
\r
1374 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1375 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1376 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1377 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
\r
1380 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1381 .amendFeatures(seqs, features, true, ap))
\r
1383 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1384 ap.av.setShowSequenceFeatures(true);
\r
1385 ap.highlightSearchResults(null);
\r
1389 public void textColour_actionPerformed()
\r
1391 SequenceGroup sg = getGroup();
\r
1394 new TextColourChooser().chooseColour(ap, sg);
\r
1398 public void colourByStructure(String pdbid)
\r
1400 Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
\r
1401 .colourSequenceFromStructure(sequence, pdbid);
\r
1403 AlignmentAnnotation an = new AlignmentAnnotation(
\r
1404 "Structure", "Coloured by "+pdbid, anots);
\r
1406 ap.av.alignment.addAnnotation(an);
\r
1407 an.createSequenceMapping(sequence, 0, true);
\r
1408 //an.adjustForAlignment();
\r
1409 ap.av.alignment.setAnnotationIndex(an,0);
\r
1411 ap.adjustAnnotationHeight();
\r
1413 sequence.addAlignmentAnnotation(an);
\r
1417 public void editSequence_actionPerformed(ActionEvent actionEvent)
\r
1419 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1423 if (sequence == null)
\r
1424 sequence = (Sequence) sg.getSequenceAt(0);
\r
1426 EditNameDialog dialog = new EditNameDialog(
\r
1427 sequence.getSequenceAsString(
\r
1429 sg.getEndRes() + 1),
\r
1435 if (dialog.accept)
\r
1437 EditCommand editCommand = new EditCommand(
\r
1438 "Edit Sequences", EditCommand.REPLACE,
\r
1440 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1441 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
\r
1444 ap.alignFrame.addHistoryItem(editCommand);
\r
1446 ap.av.firePropertyChange("alignment", null,
\r
1447 ap.av.getAlignment().getSequences());
\r