2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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 Softwarechang
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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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21 import java.beans.*;
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26 import java.awt.datatransfer.*;
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27 import java.awt.event.*;
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28 import java.awt.print.*;
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29 import javax.swing.*;
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31 import jalview.analysis.*;
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32 import jalview.datamodel.*;
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33 import jalview.io.*;
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34 import jalview.jbgui.*;
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35 import jalview.schemes.*;
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36 import jalview.ws.*;
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37 import javax.swing.event.AncestorEvent;
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43 * @version $Revision$
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45 public class AlignFrame
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46 extends GAlignFrame implements ClipboardOwner
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48 /** DOCUMENT ME!! */
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49 public static final int NEW_WINDOW_WIDTH = 700;
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51 /** DOCUMENT ME!! */
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52 public static final int NEW_WINDOW_HEIGHT = 500;
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53 AlignmentPanel alignPanel;
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54 AlignViewport viewport;
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56 Vector viewports = new Vector();
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57 Vector alignPanels = new Vector();
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59 /** DOCUMENT ME!! */
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60 public String currentFileFormat = null;
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61 Stack historyList = new Stack();
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62 Stack redoList = new Stack();
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63 private int treeCount = 0;
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67 * Creates a new AlignFrame object.
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69 * @param al DOCUMENT ME!
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71 public AlignFrame(AlignmentI al)
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73 viewport = new AlignViewport(al);
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74 viewports.add(viewport);
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77 if(viewport.vconsensus==null)
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79 //Out of memory calculating consensus.
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80 BLOSUM62Colour.setEnabled(false);
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81 PIDColour.setEnabled(false);
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82 conservationMenuItem.setEnabled(false);
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83 modifyConservation.setEnabled(false);
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84 abovePIDThreshold.setEnabled(false);
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85 modifyPID.setEnabled(false);
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88 alignPanel = new AlignmentPanel(this, viewport);
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89 alignPanels.add(alignPanel);
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91 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
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93 if(sortby.equals("Id"))
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94 sortIDMenuItem_actionPerformed(null);
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95 else if(sortby.equals("Pairwise Identity"))
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96 sortPairwiseMenuItem_actionPerformed(null);
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98 // remove(tabbedPane);
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99 getContentPane().add(alignPanel, BorderLayout.CENTER);
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103 // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
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106 /////////////////////////
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107 if(al.getDataset()==null)
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109 al.setDataset(null);
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111 // AlignViewport ds = new AlignViewport(al.getDataset(), true);
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112 // AlignmentPanel dap = new AlignmentPanel(this, ds);
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113 // tabbedPane.add("Dataset", dap);
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114 // viewports.add(ds);
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115 // alignPanels.add(dap);
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116 /////////////////////////
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119 viewport.addPropertyChangeListener(new PropertyChangeListener()
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121 public void propertyChange(PropertyChangeEvent evt)
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123 if (evt.getPropertyName().equals("alignment"))
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125 alignmentChanged();
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131 if (Desktop.desktop != null)
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133 addServiceListeners();
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134 setGUINucleotide(al.isNucleotide());
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138 /* Set up intrinsic listeners for dynamically generated GUI bits. */
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139 private void addServiceListeners()
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141 final java.beans.PropertyChangeListener thisListener;
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142 // Do this once to get current state
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143 BuildWebServiceMenu();
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144 Desktop.discoverer.addPropertyChangeListener(
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145 thisListener = new java.beans.PropertyChangeListener()
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147 public void propertyChange(PropertyChangeEvent evt)
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149 // System.out.println("Discoverer property change.");
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150 if (evt.getPropertyName().equals("services"))
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152 // System.out.println("Rebuilding web service menu");
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153 BuildWebServiceMenu();
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157 addInternalFrameListener(new javax.swing.event.
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158 InternalFrameAdapter()
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160 public void internalFrameClosed(
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161 javax.swing.event.InternalFrameEvent evt)
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163 // System.out.println("deregistering discoverer listener");
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164 Desktop.discoverer.removePropertyChangeListener(thisListener);
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165 closeMenuItem_actionPerformed(null);
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172 public void setGUINucleotide(boolean nucleotide)
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174 showTranslation.setVisible( nucleotide );
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175 sequenceFeatures.setVisible(!nucleotide );
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176 featureSettings.setVisible( !nucleotide );
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177 conservationMenuItem.setVisible( !nucleotide );
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178 modifyConservation.setVisible( !nucleotide );
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180 //Deal with separators
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181 //Remember AlignFrame always starts as protein
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184 viewMenu.remove(viewMenu.getItemCount()-2);
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188 calculateMenu.remove(calculateMenu.getItemCount()-2);
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194 Added so Castor Mapping file can obtain Jalview Version
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196 public String getVersion()
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198 return jalview.bin.Cache.getProperty("VERSION");
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205 * @param String DOCUMENT ME!
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208 public void parseGroupsFile(String file)
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212 BufferedReader in = new BufferedReader(new FileReader(file));
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213 SequenceI seq = null;
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214 String line, type, desc, token;
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216 int index, start, end;
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217 StringTokenizer st;
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218 SequenceFeature sf;
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219 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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221 while ( (line = in.readLine()) != null)
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224 st = new StringTokenizer(line, "\t");
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225 if (st.countTokens() == 2)
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227 type = st.nextToken();
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228 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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229 fr.setColour(type, ucs.findColour("A"));
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233 while (st.hasMoreElements())
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235 desc = st.nextToken();
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236 token = st.nextToken();
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237 if (!token.equals("ID_NOT_SPECIFIED"))
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239 index = viewport.alignment.findIndex(viewport.alignment.findName(
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245 index = Integer.parseInt(st.nextToken());
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248 start = Integer.parseInt(st.nextToken());
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249 end = Integer.parseInt(st.nextToken());
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251 seq = viewport.alignment.getSequenceAt(index);
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252 start = seq.findIndex(start) - 1;
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253 end = seq.findIndex(end) - 1;
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255 type = st.nextToken();
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257 if (fr.getColour(type) == null)
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259 // Probably the old style groups file
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260 UserColourScheme ucs = new UserColourScheme(type);
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261 fr.setColour(type, ucs.findColour("A"));
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265 sf = new SequenceFeature(type, desc, "", start, end);
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267 seq.addSequenceFeature(sf);
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270 // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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271 // sg.addSequence(seq, false);
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273 // viewport.alignment.addGroup(sg);
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278 viewport.showSequenceFeatures = true;
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279 ((Alignment)viewport.alignment).featuresAdded = true;
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281 alignPanel.repaint();
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284 catch (Exception ex)
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286 System.out.println("Error parsing groups file: " + ex);
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290 public void fetchSequence_actionPerformed(ActionEvent e)
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292 new SequenceFetcher(this);
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299 * @param e DOCUMENT ME!
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301 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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303 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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308 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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313 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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314 }, currentFileFormat);
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316 chooser.setAcceptAllFileFilterUsed(false);
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317 chooser.setFileView(new JalviewFileView());
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318 chooser.setDialogTitle("Save Alignment to file");
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319 chooser.setToolTipText("Save");
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321 int value = chooser.showSaveDialog(this);
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323 if (value == JalviewFileChooser.APPROVE_OPTION)
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325 currentFileFormat = chooser.getSelectedFormat();
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327 if (currentFileFormat == null)
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329 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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330 "You must select a file format before saving!",
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331 "File format not specified",
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332 JOptionPane.WARNING_MESSAGE);
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333 value = chooser.showSaveDialog(this);
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337 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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338 currentFileFormat);
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340 String choice = chooser.getSelectedFile().getPath();
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341 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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343 saveAlignment(choice, currentFileFormat);
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347 public boolean saveAlignment(String file, String format)
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349 if (format.equalsIgnoreCase("Jalview"))
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351 String shortName = title;
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353 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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355 shortName = shortName.substring(shortName.lastIndexOf(
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356 java.io.File.separatorChar) + 1);
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359 Jalview2XML.SaveAlignment(this, file, shortName);
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361 // USE Jalview2XML to save this file
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366 String output = new FormatAdapter().formatSequences(format,
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367 viewport.getAlignment().
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369 if (output == null)
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376 java.io.PrintWriter out = new java.io.PrintWriter(
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377 new java.io.FileWriter(file));
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383 catch (Exception ex)
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385 ex.printStackTrace();
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394 * @param e DOCUMENT ME!
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396 protected void outputText_actionPerformed(ActionEvent e)
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398 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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399 Desktop.addInternalFrame(cap,
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400 "Alignment output - " + e.getActionCommand(), 600,
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402 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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403 viewport.getAlignment().
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410 * @param e DOCUMENT ME!
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412 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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414 new HTMLOutput(viewport,
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415 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
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416 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
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419 public void createImageMap(File file, String image)
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421 alignPanel.makePNGImageMap(file, image);
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427 * @param e DOCUMENT ME!
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429 public void createPNG(File f)
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431 alignPanel.makePNG(f);
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437 * @param e DOCUMENT ME!
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439 public void createEPS(File f)
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441 alignPanel.makeEPS(f);
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447 * @param e DOCUMENT ME!
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449 public void printMenuItem_actionPerformed(ActionEvent e)
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451 //Putting in a thread avoids Swing painting problems
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452 PrintThread thread = new PrintThread();
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459 * @param e DOCUMENT ME!
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461 public void closeMenuItem_actionPerformed(ActionEvent e)
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465 PaintRefresher.components.remove(viewport.alignment);
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466 this.setClosed(true);
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468 catch (Exception ex)
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476 void updateEditMenuBar()
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478 if (historyList.size() > 0)
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480 undoMenuItem.setEnabled(true);
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482 HistoryItem hi = (HistoryItem) historyList.peek();
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483 undoMenuItem.setText("Undo " + hi.getDescription());
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487 undoMenuItem.setEnabled(false);
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488 undoMenuItem.setText("Undo");
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491 if (redoList.size() > 0)
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493 redoMenuItem.setEnabled(true);
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495 HistoryItem hi = (HistoryItem) redoList.peek();
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496 redoMenuItem.setText("Redo " + hi.getDescription());
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500 redoMenuItem.setEnabled(false);
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501 redoMenuItem.setText("Redo");
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508 * @param hi DOCUMENT ME!
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510 public void addHistoryItem(HistoryItem hi)
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512 historyList.push(hi);
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513 updateEditMenuBar();
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519 * @param e DOCUMENT ME!
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521 protected void undoMenuItem_actionPerformed(ActionEvent e)
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523 HistoryItem hi = (HistoryItem) historyList.pop();
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524 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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525 HistoryItem.HIDE));
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526 restoreHistoryItem(hi);
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527 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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533 * @param e DOCUMENT ME!
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535 protected void redoMenuItem_actionPerformed(ActionEvent e)
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537 HistoryItem hi = (HistoryItem) redoList.pop();
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538 restoreHistoryItem(hi);
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539 updateEditMenuBar();
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540 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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543 // used by undo and redo
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544 void restoreHistoryItem(HistoryItem hi)
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546 if (hi.getType() == HistoryItem.SORT)
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548 for (int i = 0; i < hi.getSequences().size(); i++)
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550 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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557 for (int i = 0; i < hi.getSequences().size(); i++)
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559 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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561 if (restore.getLength() == 0)
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563 restore.setSequence(hi.getHidden().elementAt(i).toString());
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564 viewport.alignment.getSequences().insertElementAt(restore,
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565 hi.getAlignIndex(i));
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569 restore.setSequence(hi.getHidden().elementAt(i).toString());
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573 if (hi.getType() == HistoryItem.PASTE)
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575 for (int i = viewport.alignment.getHeight() - 1;
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576 i > (hi.getSequences().size() - 1); i--)
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578 viewport.alignment.deleteSequence(i);
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583 updateEditMenuBar();
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585 viewport.firePropertyChange("alignment", null,
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586 viewport.getAlignment().getSequences());
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592 * @param up DOCUMENT ME!
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594 public void moveSelectedSequences(boolean up)
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596 SequenceGroup sg = viewport.getSelectionGroup();
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605 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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607 SequenceI seq = viewport.alignment.getSequenceAt(i);
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609 if (!sg.sequences.contains(seq))
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614 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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616 if (sg.sequences.contains(temp))
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621 viewport.alignment.getSequences().setElementAt(temp, i);
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622 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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627 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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629 SequenceI seq = viewport.alignment.getSequenceAt(i);
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631 if (!sg.sequences.contains(seq))
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636 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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638 if (sg.sequences.contains(temp))
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643 viewport.alignment.getSequences().setElementAt(temp, i);
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644 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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648 alignPanel.repaint();
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651 public void lostOwnership(Clipboard clipboard, Transferable contents)
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653 Desktop.jalviewClipboard = null;
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660 * @param e DOCUMENT ME!
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662 protected void copy_actionPerformed(ActionEvent e)
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664 if (viewport.getSelectionGroup() == null)
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669 SequenceGroup sg = viewport.getSelectionGroup();
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671 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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673 Hashtable orderedSeqs = new Hashtable();
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674 SequenceI[] seqs = new SequenceI[sg.getSize()];
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676 for (int i = 0; i < sg.getSize(); i++)
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678 SequenceI seq = sg.getSequenceAt(i);
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679 int index = viewport.alignment.findIndex(seq);
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680 orderedSeqs.put(index + "", seq);
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683 int index = 0, startRes, endRes;
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686 for (int i = 0; i < sg.getSize(); i++)
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688 SequenceI seq = null;
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690 while (seq == null)
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692 if (orderedSeqs.containsKey(index + ""))
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694 seq = (SequenceI) orderedSeqs.get(index + "");
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706 //Returns residue following index if gap
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707 startRes = seq.findPosition(sg.getStartRes());
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710 //Need to find the residue preceeding index if gap
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713 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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715 ch = seq.getCharAt(j);
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716 if (!jalview.util.Comparison.isGap( (ch)))
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724 endRes += seq.getStart() - 1;
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727 seqs[i] = new Sequence(seq.getName(),
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728 seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
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731 seqs[i].setDescription(seq.getDescription());
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732 seqs[i].setDBRef(seq.getDBRef());
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733 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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734 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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738 FastaFile ff = new FastaFile();
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739 ff.addJVSuffix( viewport.showJVSuffix );
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740 c.setContents(new StringSelection( ff.print(seqs)), this);
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741 Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};
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747 * @param e DOCUMENT ME!
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749 protected void pasteNew_actionPerformed(ActionEvent e)
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757 * @param e DOCUMENT ME!
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759 protected void pasteThis_actionPerformed(ActionEvent e)
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761 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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762 HistoryItem.PASTE));
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769 * @param newAlignment DOCUMENT ME!
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771 void paste(boolean newAlignment)
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775 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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776 Transferable contents = c.getContents(this);
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778 if (contents == null)
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783 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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787 String format = IdentifyFile.Identify(str, "Paste");
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788 SequenceI[] sequences;
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790 if(Desktop.jalviewClipboard!=null)
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792 // The clipboard was filled from within Jalview, we must use the sequences
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793 // And dataset from the copied alignment
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794 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
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798 sequences = new FormatAdapter().readFile(str, "Paste", format);
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804 Alignment alignment = new Alignment(sequences);
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806 if(Desktop.jalviewClipboard!=null)
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807 alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
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809 alignment.setDataset( null );
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812 AlignFrame af = new AlignFrame(alignment);
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813 String newtitle = new String("Copied sequences");
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815 if (title.startsWith("Copied sequences"))
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821 newtitle = newtitle.concat("- from " + title);
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824 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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825 NEW_WINDOW_HEIGHT);
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830 for (int i = 0; i < sequences.length; i++)
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832 viewport.alignment.addSequence(sequences[i]);
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833 if(sequences[i].getDatasetSequence()==null)
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835 ////////////////////////////
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836 //Datset needs extension;
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837 /////////////////////////////
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838 Sequence ds = new Sequence(sequences[i].getName(),
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839 AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
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840 sequences[i].getStart(),
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841 sequences[i].getEnd());
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842 sequences[i].setDatasetSequence(ds);
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843 viewport.alignment.getDataset().addSequence(ds);
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849 viewport.setEndSeq(viewport.alignment.getHeight());
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850 viewport.alignment.getWidth();
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851 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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854 catch (Exception ex)
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856 // could be anything being pasted in here
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865 * @param e DOCUMENT ME!
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867 protected void cut_actionPerformed(ActionEvent e)
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869 copy_actionPerformed(null);
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870 delete_actionPerformed(null);
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876 * @param e DOCUMENT ME!
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878 protected void delete_actionPerformed(ActionEvent e)
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881 if (viewport.getSelectionGroup() == null)
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886 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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887 HistoryItem.HIDE));
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889 SequenceGroup sg = viewport.getSelectionGroup();
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890 boolean allSequences = false;
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891 if (sg.sequences.size() == viewport.alignment.getHeight())
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893 allSequences = true;
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896 for (int i = 0; i < sg.sequences.size(); i++)
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898 SequenceI seq = sg.getSequenceAt(i);
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899 int index = viewport.getAlignment().findIndex(seq);
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900 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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902 // If the cut affects all sequences, remove highlighted columns
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905 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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906 sg.getEndRes() + 1);
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909 if (seq.getSequence().length() < 1)
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911 viewport.getAlignment().deleteSequence(seq);
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915 viewport.getAlignment().getSequences().setElementAt(seq, index);
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919 viewport.setSelectionGroup(null);
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920 viewport.alignment.deleteGroup(sg);
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922 viewport.firePropertyChange("alignment", null,
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923 viewport.getAlignment().getSequences());
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927 if (viewport.getAlignment().getHeight() < 1)
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931 this.setClosed(true);
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933 catch (Exception ex)
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942 * @param e DOCUMENT ME!
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944 protected void deleteGroups_actionPerformed(ActionEvent e)
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946 viewport.alignment.deleteAllGroups();
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947 viewport.setSelectionGroup(null);
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948 alignPanel.repaint();
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954 * @param e DOCUMENT ME!
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956 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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958 SequenceGroup sg = new SequenceGroup();
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960 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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963 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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966 sg.setEndRes(viewport.alignment.getWidth() - 1);
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967 viewport.setSelectionGroup(sg);
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968 PaintRefresher.Refresh(null, viewport.alignment);
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974 * @param e DOCUMENT ME!
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976 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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978 viewport.setSelectionGroup(null);
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979 viewport.getColumnSelection().clear();
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980 viewport.setSelectionGroup(null);
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981 alignPanel.annotationPanel.activeRes = null;
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982 PaintRefresher.Refresh(null, viewport.alignment);
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988 * @param e DOCUMENT ME!
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990 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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992 SequenceGroup sg = viewport.getSelectionGroup();
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996 selectAllSequenceMenuItem_actionPerformed(null);
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1001 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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1004 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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1007 PaintRefresher.Refresh(null, viewport.alignment);
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1013 * @param e DOCUMENT ME!
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1015 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1017 ColumnSelection colSel = viewport.getColumnSelection();
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1019 if (colSel.size() > 0)
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1021 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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1022 HistoryItem.HIDE));
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1024 int min = colSel.getMin();
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1025 viewport.getAlignment().trimLeft(min);
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1026 colSel.compensateForEdit(0, min);
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1028 if (viewport.getSelectionGroup() != null)
\r
1030 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1033 Vector groups = viewport.alignment.getGroups();
\r
1035 for (int i = 0; i < groups.size(); i++)
\r
1037 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1039 if (!sg.adjustForRemoveLeft(min))
\r
1041 viewport.alignment.deleteGroup(sg);
\r
1045 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1052 * @param e DOCUMENT ME!
\r
1054 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1056 ColumnSelection colSel = viewport.getColumnSelection();
\r
1058 if (colSel.size() > 0)
\r
1060 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1061 HistoryItem.HIDE));
\r
1063 int max = colSel.getMax();
\r
1064 viewport.getAlignment().trimRight(max);
\r
1066 if (viewport.getSelectionGroup() != null)
\r
1068 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1071 Vector groups = viewport.alignment.getGroups();
\r
1073 for (int i = 0; i < groups.size(); i++)
\r
1075 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1077 if (!sg.adjustForRemoveRight(max))
\r
1079 viewport.alignment.deleteGroup(sg);
\r
1083 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1090 * @param e DOCUMENT ME!
\r
1092 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1094 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1095 viewport.alignment, HistoryItem.HIDE));
\r
1097 //This is to maintain viewport position on first residue
\r
1098 //of first sequence
\r
1099 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1100 int startRes = seq.findPosition(viewport.startRes);
\r
1102 viewport.getAlignment().removeGaps();
\r
1104 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1106 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1112 * @param e DOCUMENT ME!
\r
1114 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1116 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1117 HistoryItem.HIDE));
\r
1119 //This is to maintain viewport position on first residue
\r
1120 //of first sequence
\r
1121 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1122 int startRes = seq.findPosition(viewport.startRes);
\r
1125 SequenceI current;
\r
1128 Vector seqs = null;
\r
1131 int end = viewport.alignment.getWidth();
\r
1133 if (viewport.getSelectionGroup() != null
\r
1134 && viewport.getSelectionGroup().sequences != null
\r
1135 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1137 seqs = viewport.getSelectionGroup().sequences;
\r
1138 start = viewport.getSelectionGroup().getStartRes();
\r
1139 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1143 seqs = viewport.alignment.getSequences();
\r
1146 for (int i = 0; i < seqs.size(); i++)
\r
1148 current = (SequenceI) seqs.elementAt(i);
\r
1149 jSize = current.getLength();
\r
1151 // Removing a range is much quicker than removing gaps
\r
1152 // one by one for long sequences
\r
1154 int rangeStart=-1, rangeEnd=-1;
\r
1158 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1160 if(rangeStart==-1)
\r
1175 current.deleteChars(rangeStart, rangeEnd);
\r
1176 j-=rangeEnd-rangeStart;
\r
1177 jSize-=rangeEnd-rangeStart;
\r
1185 while (j < end && j < jSize);
\r
1188 current.deleteChars(rangeStart, rangeEnd);
\r
1192 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1194 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1197 public void alignmentChanged()
\r
1199 if(viewport.vconsensus!=null)
\r
1201 viewport.updateConsensus();
\r
1202 viewport.updateConservation();
\r
1204 resetAllColourSchemes();
\r
1205 if(alignPanel.overviewPanel!=null)
\r
1206 alignPanel.overviewPanel.updateOverviewImage();
\r
1208 Provenance prov = viewport.alignment.getProvenance();
\r
1211 prov = new Provenance();
\r
1212 viewport.alignment.setProvenance(prov);
\r
1215 prov.addEntry("Me",
\r
1216 "Edited in Jalview", new java.util.Date(), "myID");
\r
1218 alignPanel.repaint();
\r
1221 void resetAllColourSchemes()
\r
1223 ColourSchemeI cs = viewport.globalColourScheme;
\r
1226 if (cs instanceof ClustalxColourScheme)
\r
1228 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1229 resetClustalX(viewport.alignment.getSequences(),
\r
1230 viewport.alignment.getWidth());
\r
1233 cs.setConsensus(viewport.vconsensus);
\r
1234 if (cs.conservationApplied())
\r
1236 Alignment al = (Alignment) viewport.alignment;
\r
1237 Conservation c = new Conservation("All",
\r
1238 ResidueProperties.propHash, 3,
\r
1239 al.getSequences(), 0,
\r
1240 al.getWidth() - 1);
\r
1242 c.verdict(false, viewport.ConsPercGaps);
\r
1244 cs.setConservation(c);
\r
1248 int s, sSize = viewport.alignment.getGroups().size();
\r
1249 for(s=0; s<sSize; s++)
\r
1251 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1252 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1254 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1256 sg.recalcConservation();
\r
1263 * @param e DOCUMENT ME!
\r
1265 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1267 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1268 HistoryItem.HIDE));
\r
1270 SequenceI current;
\r
1271 int Width = viewport.getAlignment().getWidth();
\r
1273 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1276 current = viewport.getAlignment().getSequenceAt(i);
\r
1278 if (current.getLength() < Width)
\r
1280 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1284 alignmentChanged();
\r
1290 * @param e DOCUMENT ME!
\r
1292 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1294 JInternalFrame frame = new JInternalFrame();
\r
1295 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1296 frame.setContentPane(finder);
\r
1297 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1298 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1304 * @param e DOCUMENT ME!
\r
1306 public void font_actionPerformed(ActionEvent e)
\r
1308 new FontChooser(alignPanel);
\r
1314 * @param e DOCUMENT ME!
\r
1316 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1318 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1320 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1321 alignPanel.repaint();
\r
1328 * @param e DOCUMENT ME!
\r
1330 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1332 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1333 alignPanel.repaint();
\r
1339 * @param e DOCUMENT ME!
\r
1341 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1343 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1344 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1345 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1346 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1347 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1348 alignPanel.repaint();
\r
1354 * @param e DOCUMENT ME!
\r
1356 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1358 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1359 alignPanel.repaint();
\r
1365 * @param e DOCUMENT ME!
\r
1367 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1369 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1370 alignPanel.repaint();
\r
1376 * @param e DOCUMENT ME!
\r
1378 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1380 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1381 alignPanel.repaint();
\r
1387 * @param e DOCUMENT ME!
\r
1389 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1391 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1392 alignPanel.repaint();
\r
1398 * @param e DOCUMENT ME!
\r
1400 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1402 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1403 alignPanel.repaint();
\r
1409 * @param e DOCUMENT ME!
\r
1411 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1413 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1414 alignPanel.repaint();
\r
1420 * @param evt DOCUMENT ME!
\r
1422 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1424 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1426 if (viewport.showSequenceFeatures &&
\r
1427 ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
\r
1429 System.out.println("new fetcher");
\r
1430 new SequenceFeatureFetcher(viewport.
\r
1435 featureSettings.setEnabled(true);
\r
1437 alignPanel.repaint();
\r
1443 * @param e DOCUMENT ME!
\r
1445 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1447 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1448 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1454 * @param e DOCUMENT ME!
\r
1456 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1458 if (alignPanel.overviewPanel != null)
\r
1463 JInternalFrame frame = new JInternalFrame();
\r
1464 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1465 frame.setContentPane(overview);
\r
1466 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1467 frame.getWidth(), frame.getHeight());
\r
1469 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1470 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1472 public void internalFrameClosed(
\r
1473 javax.swing.event.InternalFrameEvent evt)
\r
1475 alignPanel.setOverviewPanel(null);
\r
1480 alignPanel.setOverviewPanel(overview);
\r
1486 * @param e DOCUMENT ME!
\r
1488 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1490 changeColour(null);
\r
1496 * @param e DOCUMENT ME!
\r
1498 public void clustalColour_actionPerformed(ActionEvent e)
\r
1500 changeColour(new ClustalxColourScheme(
\r
1501 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1507 * @param e DOCUMENT ME!
\r
1509 public void zappoColour_actionPerformed(ActionEvent e)
\r
1511 changeColour(new ZappoColourScheme());
\r
1517 * @param e DOCUMENT ME!
\r
1519 public void taylorColour_actionPerformed(ActionEvent e)
\r
1521 changeColour(new TaylorColourScheme());
\r
1527 * @param e DOCUMENT ME!
\r
1529 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1531 changeColour(new HydrophobicColourScheme());
\r
1537 * @param e DOCUMENT ME!
\r
1539 public void helixColour_actionPerformed(ActionEvent e)
\r
1541 changeColour(new HelixColourScheme());
\r
1547 * @param e DOCUMENT ME!
\r
1549 public void strandColour_actionPerformed(ActionEvent e)
\r
1551 changeColour(new StrandColourScheme());
\r
1557 * @param e DOCUMENT ME!
\r
1559 public void turnColour_actionPerformed(ActionEvent e)
\r
1561 changeColour(new TurnColourScheme());
\r
1567 * @param e DOCUMENT ME!
\r
1569 public void buriedColour_actionPerformed(ActionEvent e)
\r
1571 changeColour(new BuriedColourScheme());
\r
1577 * @param e DOCUMENT ME!
\r
1579 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1581 changeColour(new NucleotideColourScheme());
\r
1587 * @param e DOCUMENT ME!
\r
1589 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1591 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1597 * @param cs DOCUMENT ME!
\r
1599 void changeColour(ColourSchemeI cs)
\r
1601 int threshold = 0;
\r
1605 if (viewport.getAbovePIDThreshold())
\r
1607 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1610 cs.setThreshold(threshold,
\r
1611 viewport.getIgnoreGapsConsensus());
\r
1613 viewport.setGlobalColourScheme(cs);
\r
1617 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1620 if (viewport.getConservationSelected())
\r
1623 Alignment al = (Alignment) viewport.alignment;
\r
1624 Conservation c = new Conservation("All",
\r
1625 ResidueProperties.propHash, 3,
\r
1626 al.getSequences(), 0,
\r
1627 al.getWidth() - 1);
\r
1630 c.verdict(false, viewport.ConsPercGaps);
\r
1632 cs.setConservation(c);
\r
1634 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1639 cs.setConservation(null);
\r
1642 cs.setConsensus(viewport.vconsensus);
\r
1645 viewport.setGlobalColourScheme(cs);
\r
1647 if (viewport.getColourAppliesToAllGroups())
\r
1649 Vector groups = viewport.alignment.getGroups();
\r
1651 for (int i = 0; i < groups.size(); i++)
\r
1653 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1661 if (cs instanceof ClustalxColourScheme)
\r
1663 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1665 else if (cs instanceof UserColourScheme)
\r
1667 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1673 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1675 catch (Exception ex)
\r
1680 if (viewport.getAbovePIDThreshold()
\r
1681 || cs instanceof PIDColourScheme
\r
1682 || cs instanceof Blosum62ColourScheme)
\r
1684 sg.cs.setThreshold(threshold,
\r
1685 viewport.getIgnoreGapsConsensus());
\r
1687 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1691 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1694 if (viewport.getConservationSelected())
\r
1696 Conservation c = new Conservation("Group",
\r
1697 ResidueProperties.propHash, 3,
\r
1699 viewport.alignment.getWidth() - 1);
\r
1701 c.verdict(false, viewport.ConsPercGaps);
\r
1702 sg.cs.setConservation(c);
\r
1705 sg.cs.setConservation(null);
\r
1709 if (alignPanel.getOverviewPanel() != null)
\r
1711 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1714 alignPanel.repaint();
\r
1720 * @param e DOCUMENT ME!
\r
1722 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1724 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1726 SliderPanel.setPIDSliderSource(alignPanel,
\r
1727 viewport.getGlobalColourScheme(),
\r
1729 SliderPanel.showPIDSlider();
\r
1736 * @param e DOCUMENT ME!
\r
1738 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1740 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1742 SliderPanel.setConservationSlider(alignPanel,
\r
1743 viewport.globalColourScheme,
\r
1745 SliderPanel.showConservationSlider();
\r
1752 * @param e DOCUMENT ME!
\r
1754 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1756 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1758 viewport.setAbovePIDThreshold(false);
\r
1759 abovePIDThreshold.setSelected(false);
\r
1761 changeColour(viewport.getGlobalColourScheme());
\r
1763 modifyConservation_actionPerformed(null);
\r
1769 * @param e DOCUMENT ME!
\r
1771 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1773 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1775 conservationMenuItem.setSelected(false);
\r
1776 viewport.setConservationSelected(false);
\r
1778 changeColour(viewport.getGlobalColourScheme());
\r
1780 modifyPID_actionPerformed(null);
\r
1786 * @param e DOCUMENT ME!
\r
1788 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1790 if (e.getActionCommand().equals("User Defined..."))
\r
1792 new UserDefinedColours(alignPanel, null);
\r
1796 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1797 getUserColourSchemes().get(e.getActionCommand());
\r
1799 changeColour(udc);
\r
1803 public void updateUserColourMenu()
\r
1806 Component[] menuItems = colourMenu.getMenuComponents();
\r
1807 int i, iSize = menuItems.length;
\r
1808 for (i = 0; i < iSize; i++)
\r
1810 if (menuItems[i].getName() != null &&
\r
1811 menuItems[i].getName().equals("USER_DEFINED"))
\r
1813 colourMenu.remove(menuItems[i]);
\r
1817 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1819 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1820 getUserColourSchemes().keys();
\r
1822 while (userColours.hasMoreElements())
\r
1824 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1825 nextElement().toString());
\r
1826 radioItem.setName("USER_DEFINED");
\r
1827 radioItem.addMouseListener(new MouseAdapter()
\r
1829 public void mousePressed(MouseEvent evt)
\r
1831 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1833 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1835 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1836 "Remove from default list?",
\r
1837 "Remove user defined colour",
\r
1838 JOptionPane.YES_NO_OPTION);
\r
1839 if(option == JOptionPane.YES_OPTION)
\r
1841 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1842 colourMenu.remove(radioItem);
\r
1845 radioItem.addActionListener(new ActionListener()
\r
1847 public void actionPerformed(ActionEvent evt)
\r
1849 userDefinedColour_actionPerformed(evt);
\r
1855 radioItem.addActionListener(new ActionListener()
\r
1857 public void actionPerformed(ActionEvent evt)
\r
1859 userDefinedColour_actionPerformed(evt);
\r
1863 colourMenu.insert(radioItem, 15);
\r
1864 colours.add(radioItem);
\r
1872 * @param e DOCUMENT ME!
\r
1874 public void PIDColour_actionPerformed(ActionEvent e)
\r
1876 changeColour(new PIDColourScheme());
\r
1882 * @param e DOCUMENT ME!
\r
1884 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1886 changeColour(new Blosum62ColourScheme());
\r
1892 * @param e DOCUMENT ME!
\r
1894 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1896 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1897 HistoryItem.SORT));
\r
1898 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1899 viewport.getAlignment().getSequenceAt(0));
\r
1900 alignPanel.repaint();
\r
1906 * @param e DOCUMENT ME!
\r
1908 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1910 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1911 HistoryItem.SORT));
\r
1912 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1913 alignPanel.repaint();
\r
1919 * @param e DOCUMENT ME!
\r
1921 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1923 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1924 HistoryItem.SORT));
\r
1926 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1927 alignPanel.repaint();
\r
1933 * @param e DOCUMENT ME!
\r
1935 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1937 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1938 JInternalFrame frame = new JInternalFrame();
\r
1939 frame.setContentPane(sp);
\r
1940 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1947 * @param e DOCUMENT ME!
\r
1949 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1951 if ( (viewport.getSelectionGroup() == null) ||
\r
1952 (viewport.getSelectionGroup().getSize() < 2))
\r
1954 JOptionPane.showInternalMessageDialog(this,
\r
1955 "You must select at least 2 sequences.",
\r
1956 "Invalid Selection",
\r
1957 JOptionPane.WARNING_MESSAGE);
\r
1961 JInternalFrame frame = new JInternalFrame();
\r
1962 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1963 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1970 * @param e DOCUMENT ME!
\r
1972 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1974 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1975 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1976 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1977 (viewport.getAlignment().getHeight() < 4))
\r
1979 JOptionPane.showInternalMessageDialog(this,
\r
1980 "Principal component analysis must take\n" +
\r
1981 "at least 4 input sequences.",
\r
1982 "Sequence selection insufficient",
\r
1983 JOptionPane.WARNING_MESSAGE);
\r
1988 new PCAPanel(viewport);
\r
1994 * @param e DOCUMENT ME!
\r
1996 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1998 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2004 * @param e DOCUMENT ME!
\r
2006 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
2008 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2014 * @param e DOCUMENT ME!
\r
2016 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2018 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2024 * @param e DOCUMENT ME!
\r
2026 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2028 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2034 * @param type DOCUMENT ME!
\r
2035 * @param pwType DOCUMENT ME!
\r
2036 * @param title DOCUMENT ME!
\r
2038 void NewTreePanel(String type, String pwType, String title)
\r
2040 final TreePanel tp;
\r
2042 if ( (viewport.getSelectionGroup() != null) &&
\r
2043 (viewport.getSelectionGroup().getSize() > 3))
\r
2046 SequenceGroup sg = viewport.getSelectionGroup();
\r
2048 /* Decide if the selection is a column region */
\r
2049 while (s < sg.sequences.size())
\r
2051 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2054 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2055 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2056 "Try using the Pad function in the edit menu,\n" +
\r
2057 "or one of the multiple sequence alignment web services.",
\r
2058 "Sequences in selection are not aligned",
\r
2059 JOptionPane.WARNING_MESSAGE);
\r
2065 title = title + " on region";
\r
2066 tp = new TreePanel(viewport,
\r
2067 viewport.getSelectionGroup().sequences, type, pwType,
\r
2068 sg.getStartRes(), sg.getEndRes());
\r
2072 //are the sequences aligned?
\r
2073 if (!viewport.alignment.isAligned())
\r
2075 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2076 "The sequences must be aligned before creating a tree.\n" +
\r
2077 "Try using the Pad function in the edit menu,\n" +
\r
2078 "or one of the multiple sequence alignment web services.",
\r
2079 "Sequences not aligned",
\r
2080 JOptionPane.WARNING_MESSAGE);
\r
2085 tp = new TreePanel(viewport,
\r
2086 viewport.getAlignment().getSequences(), type, pwType,
\r
2088 viewport.alignment.getWidth());
\r
2091 addTreeMenuItem(tp, title);
\r
2092 viewport.setCurrentTree(tp.getTree());
\r
2094 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2100 * @param title DOCUMENT ME!
\r
2101 * @param order DOCUMENT ME!
\r
2103 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2105 final JMenuItem item = new JMenuItem("by " + title);
\r
2107 item.addActionListener(new java.awt.event.ActionListener()
\r
2109 public void actionPerformed(ActionEvent e)
\r
2111 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2112 HistoryItem.SORT));
\r
2114 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2115 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2116 alignPanel.repaint();
\r
2122 * Maintain the Order by->Displayed Tree menu.
\r
2123 * Creates a new menu item for a TreePanel with an appropriate
\r
2124 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2125 * to remove the menu item when the treePanel is closed, and adjust
\r
2126 * the tree leaf to sequence mapping when the alignment is modified.
\r
2127 * @param treePanel Displayed tree window.
\r
2128 * @param title SortBy menu item title.
\r
2130 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2132 final JMenuItem item = new JMenuItem(title);
\r
2136 if (treeCount == 1)
\r
2138 sort.add(sortByTreeMenu);
\r
2141 sortByTreeMenu.add(item);
\r
2142 item.addActionListener(new java.awt.event.ActionListener()
\r
2144 public void actionPerformed(ActionEvent e)
\r
2146 addHistoryItem(new HistoryItem("Tree Sort",
\r
2147 viewport.alignment, HistoryItem.SORT));
\r
2148 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2149 treePanel.getTree());
\r
2150 alignPanel.repaint();
\r
2154 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2155 InternalFrameAdapter()
\r
2157 public void internalFrameClosed(
\r
2158 javax.swing.event.InternalFrameEvent evt)
\r
2161 sortByTreeMenu.remove(item);
\r
2163 if (treeCount == 0)
\r
2165 sort.remove(sortByTreeMenu);
\r
2173 * Work out whether the whole set of sequences
\r
2174 * or just the selected set will be submitted for multiple alignment.
\r
2177 private SequenceI[] gatherSequencesForAlignment()
\r
2179 // Now, check we have enough sequences
\r
2180 SequenceI[] msa = null;
\r
2182 if ( (viewport.getSelectionGroup() != null) &&
\r
2183 (viewport.getSelectionGroup().getSize() > 1))
\r
2185 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2186 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2188 msa = new SequenceI[sz = seqs.getSize()];
\r
2190 for (int i = 0; i < sz; i++)
\r
2192 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2197 Vector seqs = viewport.getAlignment().getSequences();
\r
2199 if (seqs.size() > 1)
\r
2201 msa = new SequenceI[seqs.size()];
\r
2203 for (int i = 0; i < seqs.size(); i++)
\r
2205 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2213 * Decides what is submitted to a secondary structure prediction service,
\r
2214 * the currently selected sequence, or the currently selected alignment
\r
2215 * (where the first sequence in the set is the one that the prediction
\r
2218 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2220 SequenceI seq = null;
\r
2221 SequenceI[] msa = null;
\r
2223 if ( (viewport.getSelectionGroup() != null) &&
\r
2224 (viewport.getSelectionGroup().getSize() > 0))
\r
2226 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2227 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2229 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2231 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2236 msa = new SequenceI[sz = seqs.getSize()];
\r
2238 for (int i = 0; i < sz; i++)
\r
2240 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2246 Vector seqs = viewport.getAlignment().getSequences();
\r
2248 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2250 seq = (SequenceI) seqs.elementAt(0);
\r
2254 msa = new SequenceI[seqs.size()];
\r
2256 for (int i = 0; i < seqs.size(); i++)
\r
2258 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2270 return new SequenceI[]
\r
2280 * @param e DOCUMENT ME!
\r
2282 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2284 // Pick the tree file
\r
2285 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2287 "LAST_DIRECTORY"));
\r
2288 chooser.setFileView(new JalviewFileView());
\r
2289 chooser.setDialogTitle("Select a newick-like tree file");
\r
2290 chooser.setToolTipText("Load a tree file");
\r
2292 int value = chooser.showOpenDialog(null);
\r
2294 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2296 String choice = chooser.getSelectedFile().getPath();
\r
2297 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2301 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2303 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2305 catch (Exception ex)
\r
2307 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2308 "Problem reading tree file",
\r
2310 JOptionPane.WARNING_MESSAGE);
\r
2311 ex.printStackTrace();
\r
2317 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2319 return ShowNewickTree(nf,title,600,500,4,5);
\r
2324 * @param nf DOCUMENT ME!
\r
2325 * @param title DOCUMENT ME!
\r
2327 * @return DOCUMENT ME!
\r
2329 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2331 TreePanel tp = null;
\r
2337 if (nf.getTree() != null)
\r
2339 tp = new TreePanel(viewport,
\r
2340 viewport.getAlignment().getSequences(), nf,
\r
2347 tp.setLocation(x,y);
\r
2350 Desktop.addInternalFrame(tp, title, w, h);
\r
2351 addTreeMenuItem(tp, title);
\r
2354 catch (Exception ex)
\r
2356 ex.printStackTrace();
\r
2367 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2368 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2369 printJob.setPrintable(alignPanel, pf);
\r
2371 if (printJob.printDialog())
\r
2377 catch (Exception PrintException)
\r
2379 PrintException.printStackTrace();
\r
2386 * Generates menu items and listener event actions for web service clients
\r
2389 public void BuildWebServiceMenu()
\r
2391 if ( (Discoverer.services != null)
\r
2392 && (Discoverer.services.size() > 0))
\r
2394 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2395 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2396 Vector wsmenu = new Vector();
\r
2397 if (msaws != null)
\r
2399 // Add any Multiple Sequence Alignment Services
\r
2400 final JMenu msawsmenu = new JMenu("Alignment");
\r
2401 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2403 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2405 final JMenuItem method = new JMenuItem(sh.getName());
\r
2406 method.addActionListener(new ActionListener()
\r
2408 public void actionPerformed(ActionEvent e)
\r
2410 SequenceI[] msa = gatherSequencesForAlignment();
\r
2411 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2412 false, true, viewport.getAlignment().getDataset());
\r
2417 msawsmenu.add(method);
\r
2418 // Deal with services that we know accept partial alignments.
\r
2419 if (sh.getName().indexOf("lustal") > -1)
\r
2421 // We know that ClustalWS can accept partial alignments for refinement.
\r
2422 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2423 methodR.addActionListener(new ActionListener()
\r
2425 public void actionPerformed(ActionEvent e)
\r
2427 SequenceI[] msa = gatherSequencesForAlignment();
\r
2428 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2429 true, true, viewport.getAlignment().getDataset());
\r
2434 msawsmenu.add(methodR);
\r
2438 wsmenu.add(msawsmenu);
\r
2440 if (secstrpr != null)
\r
2442 // Add any secondary structure prediction services
\r
2443 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2444 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2446 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2448 final JMenuItem method = new JMenuItem(sh.getName());
\r
2449 method.addActionListener(new ActionListener()
\r
2451 public void actionPerformed(ActionEvent e)
\r
2453 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2454 if (msa.length == 1)
\r
2456 // Single Sequence prediction
\r
2457 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2461 if (msa.length > 1)
\r
2463 // Single Sequence prediction
\r
2464 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2470 secstrmenu.add(method);
\r
2472 wsmenu.add(secstrmenu);
\r
2474 this.webService.removeAll();
\r
2475 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2477 webService.add( (JMenu) wsmenu.get(i));
\r
2482 this.webService.removeAll();
\r
2483 this.webService.add(this.webServiceNoServices);
\r
2485 // TODO: add in rediscovery function
\r
2486 // TODO: reduce code redundancy.
\r
2487 // TODO: group services by location as well as function.
\r
2490 /* public void vamsasStore_actionPerformed(ActionEvent e)
\r
2492 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2493 getProperty("LAST_DIRECTORY"));
\r
2495 chooser.setFileView(new JalviewFileView());
\r
2496 chooser.setDialogTitle("Export to Vamsas file");
\r
2497 chooser.setToolTipText("Export");
\r
2499 int value = chooser.showSaveDialog(this);
\r
2501 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2503 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2504 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
2505 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
2509 public void featureSettings_actionPerformed(ActionEvent e)
\r
2511 new FeatureSettings(viewport, alignPanel);
\r
2516 public void showTranslation_actionPerformed(ActionEvent e)
\r
2518 int s, sSize = viewport.alignment.getHeight();
\r
2519 SequenceI [] newSeq = new SequenceI[sSize];
\r
2522 StringBuffer protein;
\r
2524 for(s=0; s<sSize; s++)
\r
2526 protein = new StringBuffer();
\r
2527 seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
\r
2528 resSize = seq.length();
\r
2529 for(res = 0; res < resSize; res+=3)
\r
2531 String codon = seq.substring(res, res+3);
\r
2532 codon = codon.replace('U', 'T');
\r
2533 String aa = ResidueProperties.codonTranslate(codon);
\r
2535 protein.append(viewport.getGapCharacter());
\r
2536 else if(aa.equals("STOP"))
\r
2537 protein.append("X");
\r
2539 protein.append( aa );
\r
2541 newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
\r
2545 AlignmentI al = new Alignment(newSeq);
\r
2546 al.setDataset(null);
\r
2549 ////////////////////////////////
\r
2550 // Copy annotations across
\r
2551 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2552 = viewport.alignment.getAlignmentAnnotation();
\r
2554 for (int i = 0; i < annotations.length; i++)
\r
2557 if (annotations[i].label.equals("Quality") ||
\r
2558 annotations[i].label.equals("Conservation") ||
\r
2559 annotations[i].label.equals("Consensus"))
\r
2565 aSize = viewport.alignment.getWidth()/3;
\r
2566 jalview.datamodel.Annotation [] anots =
\r
2567 new jalview.datamodel.Annotation[aSize];
\r
2569 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2571 if( annotations[i].annotations[a]==null
\r
2572 || annotations[i].annotations[a]==null)
\r
2575 anots[a/3] = new Annotation(
\r
2576 annotations[i].annotations[a].displayCharacter,
\r
2577 annotations[i].annotations[a].description,
\r
2578 annotations[i].annotations[a].secondaryStructure,
\r
2579 annotations[i].annotations[a].value,
\r
2580 annotations[i].annotations[a].colour);
\r
2583 jalview.datamodel.AlignmentAnnotation aa
\r
2584 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2585 annotations[i].description, anots );
\r
2586 al.addAnnotation(aa);
\r
2590 AlignFrame af = new AlignFrame(al);
\r
2591 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2593 NEW_WINDOW_HEIGHT);
\r
2596 // AlignViewport newViewport = new AlignViewport(al);
\r
2597 // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2598 // tabbedPane.add("Protein", ap);
\r
2599 // viewports.add(newViewport);
\r
2600 // alignPanels.add(ap);
\r
2603 /////////////////////////
\r
2605 // AlignViewport ds = new AlignViewport(al.getDataset());
\r
2606 // ds.setDataset(true);
\r
2607 // AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2608 // tabbedPane.add("Dataset", dap);
\r
2609 // viewports.add(ds);
\r
2610 // alignPanels.add(dap);
\r
2611 /////////////////////////
\r
2616 /*public void tabSelected()
\r
2618 int index = tabbedPane.getSelectedIndex();
\r
2619 viewport = (AlignViewport)viewports.elementAt(index);
\r
2620 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r