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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101 setGUINucleotide(al.isNucleotide());
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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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130 if(Desktop.desktop!=null)
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131 addServiceListeners();
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134 /* Set up intrinsic listeners for dynamically generated GUI bits. */
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135 private void addServiceListeners()
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137 final java.beans.PropertyChangeListener thisListener;
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138 // Do this once to get current state
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139 BuildWebServiceMenu();
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140 Desktop.discoverer.addPropertyChangeListener(
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141 thisListener = new java.beans.PropertyChangeListener()
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143 public void propertyChange(PropertyChangeEvent evt)
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145 // System.out.println("Discoverer property change.");
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146 if (evt.getPropertyName().equals("services"))
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148 // System.out.println("Rebuilding web service menu");
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149 BuildWebServiceMenu();
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153 addInternalFrameListener(new javax.swing.event.
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154 InternalFrameAdapter()
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156 public void internalFrameClosed(
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157 javax.swing.event.InternalFrameEvent evt)
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159 // System.out.println("deregistering discoverer listener");
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160 Desktop.discoverer.removePropertyChangeListener(thisListener);
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161 closeMenuItem_actionPerformed(null);
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168 public void setGUINucleotide(boolean nucleotide)
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170 showTranslation.setVisible( nucleotide );
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171 sequenceFeatures.setVisible(!nucleotide );
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172 featureSettings.setVisible( !nucleotide );
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173 conservationMenuItem.setVisible( !nucleotide );
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174 modifyConservation.setVisible( !nucleotide );
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176 //Deal with separators
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177 //Remember AlignFrame always starts as protein
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180 viewMenu.remove(viewMenu.getItemCount()-2);
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184 calculateMenu.remove(calculateMenu.getItemCount()-2);
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190 Added so Castor Mapping file can obtain Jalview Version
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192 public String getVersion()
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194 return jalview.bin.Cache.getProperty("VERSION");
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201 * @param String DOCUMENT ME!
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204 public void parseGroupsFile(String file)
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208 BufferedReader in = new BufferedReader(new FileReader(file));
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209 SequenceI seq = null;
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210 String line, type, desc, token;
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212 int index, start, end;
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213 StringTokenizer st;
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214 SequenceFeature sf;
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215 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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217 while ( (line = in.readLine()) != null)
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220 st = new StringTokenizer(line, "\t");
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221 if (st.countTokens() == 2)
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223 type = st.nextToken();
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224 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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225 fr.setColour(type, ucs.findColour("A"));
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229 while (st.hasMoreElements())
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231 desc = st.nextToken();
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232 token = st.nextToken();
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233 if (!token.equals("ID_NOT_SPECIFIED"))
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235 index = viewport.alignment.findIndex(viewport.alignment.findName(
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241 index = Integer.parseInt(st.nextToken());
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244 start = Integer.parseInt(st.nextToken());
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245 end = Integer.parseInt(st.nextToken());
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247 seq = viewport.alignment.getSequenceAt(index);
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248 start = seq.findIndex(start) - 1;
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249 end = seq.findIndex(end) - 1;
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251 type = st.nextToken();
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253 if (fr.getColour(type) == null)
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255 // Probably the old style groups file
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256 UserColourScheme ucs = new UserColourScheme(type);
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257 fr.setColour(type, ucs.findColour("A"));
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261 sf = new SequenceFeature(type, desc, "", start, end);
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263 seq.addSequenceFeature(sf);
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266 // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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267 // sg.addSequence(seq, false);
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269 // viewport.alignment.addGroup(sg);
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274 viewport.showSequenceFeatures = true;
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275 ((Alignment)viewport.alignment).featuresAdded = true;
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277 alignPanel.repaint();
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280 catch (Exception ex)
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282 System.out.println("Error parsing groups file: " + ex);
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286 public void fetchSequence_actionPerformed(ActionEvent e)
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288 new SequenceFetcher(this);
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295 * @param e DOCUMENT ME!
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297 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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299 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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304 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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309 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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310 }, currentFileFormat);
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312 chooser.setAcceptAllFileFilterUsed(false);
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313 chooser.setFileView(new JalviewFileView());
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314 chooser.setDialogTitle("Save Alignment to file");
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315 chooser.setToolTipText("Save");
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317 int value = chooser.showSaveDialog(this);
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319 if (value == JalviewFileChooser.APPROVE_OPTION)
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321 currentFileFormat = chooser.getSelectedFormat();
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323 if (currentFileFormat == null)
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325 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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326 "You must select a file format before saving!",
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327 "File format not specified",
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328 JOptionPane.WARNING_MESSAGE);
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329 value = chooser.showSaveDialog(this);
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333 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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334 currentFileFormat);
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336 String choice = chooser.getSelectedFile().getPath();
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337 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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339 saveAlignment(choice, currentFileFormat);
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343 public boolean saveAlignment(String file, String format)
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345 if (format.equalsIgnoreCase("Jalview"))
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347 String shortName = title;
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349 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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351 shortName = shortName.substring(shortName.lastIndexOf(
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352 java.io.File.separatorChar) + 1);
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355 Jalview2XML.SaveAlignment(this, file, shortName);
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357 // USE Jalview2XML to save this file
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362 String output = new FormatAdapter().formatSequences(format,
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363 viewport.getAlignment().
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365 if (output == null)
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372 java.io.PrintWriter out = new java.io.PrintWriter(
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373 new java.io.FileWriter(file));
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379 catch (Exception ex)
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381 ex.printStackTrace();
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390 * @param e DOCUMENT ME!
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392 protected void outputText_actionPerformed(ActionEvent e)
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394 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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395 Desktop.addInternalFrame(cap,
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396 "Alignment output - " + e.getActionCommand(), 600,
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398 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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399 viewport.getAlignment().
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406 * @param e DOCUMENT ME!
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408 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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410 new HTMLOutput(viewport,
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411 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
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412 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
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415 public void createImageMap(File file, String image)
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417 alignPanel.makePNGImageMap(file, image);
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423 * @param e DOCUMENT ME!
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425 public void createPNG(File f)
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427 alignPanel.makePNG(f);
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433 * @param e DOCUMENT ME!
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435 public void createEPS(File f)
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437 alignPanel.makeEPS(f);
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443 * @param e DOCUMENT ME!
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445 public void printMenuItem_actionPerformed(ActionEvent e)
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447 //Putting in a thread avoids Swing painting problems
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448 PrintThread thread = new PrintThread();
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455 * @param e DOCUMENT ME!
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457 public void closeMenuItem_actionPerformed(ActionEvent e)
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461 PaintRefresher.components.remove(viewport.alignment);
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462 this.setClosed(true);
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464 catch (Exception ex)
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472 void updateEditMenuBar()
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474 if (historyList.size() > 0)
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476 undoMenuItem.setEnabled(true);
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478 HistoryItem hi = (HistoryItem) historyList.peek();
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479 undoMenuItem.setText("Undo " + hi.getDescription());
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483 undoMenuItem.setEnabled(false);
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484 undoMenuItem.setText("Undo");
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487 if (redoList.size() > 0)
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489 redoMenuItem.setEnabled(true);
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491 HistoryItem hi = (HistoryItem) redoList.peek();
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492 redoMenuItem.setText("Redo " + hi.getDescription());
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496 redoMenuItem.setEnabled(false);
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497 redoMenuItem.setText("Redo");
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504 * @param hi DOCUMENT ME!
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506 public void addHistoryItem(HistoryItem hi)
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508 historyList.push(hi);
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509 updateEditMenuBar();
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515 * @param e DOCUMENT ME!
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517 protected void undoMenuItem_actionPerformed(ActionEvent e)
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519 HistoryItem hi = (HistoryItem) historyList.pop();
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520 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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521 HistoryItem.HIDE));
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522 restoreHistoryItem(hi);
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523 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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529 * @param e DOCUMENT ME!
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531 protected void redoMenuItem_actionPerformed(ActionEvent e)
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533 HistoryItem hi = (HistoryItem) redoList.pop();
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534 restoreHistoryItem(hi);
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535 updateEditMenuBar();
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536 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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539 // used by undo and redo
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540 void restoreHistoryItem(HistoryItem hi)
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542 if (hi.getType() == HistoryItem.SORT)
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544 for (int i = 0; i < hi.getSequences().size(); i++)
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546 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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553 for (int i = 0; i < hi.getSequences().size(); i++)
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555 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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557 if (restore.getLength() == 0)
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559 restore.setSequence(hi.getHidden().elementAt(i).toString());
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560 viewport.alignment.getSequences().insertElementAt(restore,
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561 hi.getAlignIndex(i));
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565 restore.setSequence(hi.getHidden().elementAt(i).toString());
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569 if (hi.getType() == HistoryItem.PASTE)
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571 for (int i = viewport.alignment.getHeight() - 1;
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572 i > (hi.getSequences().size() - 1); i--)
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574 viewport.alignment.deleteSequence(i);
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579 updateEditMenuBar();
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581 viewport.firePropertyChange("alignment", null,
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582 viewport.getAlignment().getSequences());
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588 * @param up DOCUMENT ME!
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590 public void moveSelectedSequences(boolean up)
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592 SequenceGroup sg = viewport.getSelectionGroup();
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601 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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603 SequenceI seq = viewport.alignment.getSequenceAt(i);
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605 if (!sg.sequences.contains(seq))
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610 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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612 if (sg.sequences.contains(temp))
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617 viewport.alignment.getSequences().setElementAt(temp, i);
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618 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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623 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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625 SequenceI seq = viewport.alignment.getSequenceAt(i);
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627 if (!sg.sequences.contains(seq))
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632 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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634 if (sg.sequences.contains(temp))
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639 viewport.alignment.getSequences().setElementAt(temp, i);
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640 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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644 alignPanel.repaint();
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647 public void lostOwnership(Clipboard clipboard, Transferable contents)
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649 Desktop.jalviewClipboard = null;
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656 * @param e DOCUMENT ME!
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658 protected void copy_actionPerformed(ActionEvent e)
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660 if (viewport.getSelectionGroup() == null)
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665 SequenceGroup sg = viewport.getSelectionGroup();
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667 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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669 Hashtable orderedSeqs = new Hashtable();
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670 SequenceI[] seqs = new SequenceI[sg.getSize()];
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672 for (int i = 0; i < sg.getSize(); i++)
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674 SequenceI seq = sg.getSequenceAt(i);
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675 int index = viewport.alignment.findIndex(seq);
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676 orderedSeqs.put(index + "", seq);
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679 int index = 0, startRes, endRes;
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682 for (int i = 0; i < sg.getSize(); i++)
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684 SequenceI seq = null;
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686 while (seq == null)
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688 if (orderedSeqs.containsKey(index + ""))
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690 seq = (SequenceI) orderedSeqs.get(index + "");
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702 //Returns residue following index if gap
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703 startRes = seq.findPosition(sg.getStartRes());
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706 //Need to find the residue preceeding index if gap
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709 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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711 ch = seq.getCharAt(j);
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712 if (!jalview.util.Comparison.isGap( (ch)))
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720 endRes += seq.getStart() - 1;
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723 seqs[i] = new Sequence(seq.getName(),
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724 seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
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727 seqs[i].setDescription(seq.getDescription());
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728 seqs[i].setDBRef(seq.getDBRef());
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729 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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730 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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734 FastaFile ff = new FastaFile();
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735 ff.addDBPrefix( viewport.showDBPrefix );
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736 ff.addJVSuffix( viewport.showJVSuffix );
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737 c.setContents(new StringSelection( ff.print(seqs)), this);
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738 Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};
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744 * @param e DOCUMENT ME!
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746 protected void pasteNew_actionPerformed(ActionEvent e)
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754 * @param e DOCUMENT ME!
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756 protected void pasteThis_actionPerformed(ActionEvent e)
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758 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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759 HistoryItem.PASTE));
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766 * @param newAlignment DOCUMENT ME!
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768 void paste(boolean newAlignment)
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772 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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773 Transferable contents = c.getContents(this);
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775 if (contents == null)
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780 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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784 String format = IdentifyFile.Identify(str, "Paste");
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785 SequenceI[] sequences;
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787 if(Desktop.jalviewClipboard!=null)
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789 // The clipboard was filled from within Jalview, we must use the sequences
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790 // And dataset from the copied alignment
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791 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
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795 sequences = new FormatAdapter().readFile(str, "Paste", format);
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801 Alignment alignment = new Alignment(sequences);
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803 if(Desktop.jalviewClipboard!=null)
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804 alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
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806 alignment.setDataset( null );
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809 AlignFrame af = new AlignFrame(alignment);
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810 String newtitle = new String("Copied sequences");
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812 if (title.startsWith("Copied sequences"))
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818 newtitle = newtitle.concat("- from " + title);
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821 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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822 NEW_WINDOW_HEIGHT);
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827 for (int i = 0; i < sequences.length; i++)
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829 viewport.alignment.addSequence(sequences[i]);
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830 if(sequences[i].getDatasetSequence()==null)
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832 ////////////////////////////
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833 //Datset needs extension;
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834 /////////////////////////////
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835 Sequence ds = new Sequence(sequences[i].getName(),
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836 AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
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837 sequences[i].getStart(),
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838 sequences[i].getEnd());
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839 sequences[i].setDatasetSequence(ds);
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840 viewport.alignment.getDataset().addSequence(ds);
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846 viewport.setEndSeq(viewport.alignment.getHeight());
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847 viewport.alignment.getWidth();
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848 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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851 catch (Exception ex)
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853 // could be anything being pasted in here
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862 * @param e DOCUMENT ME!
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864 protected void cut_actionPerformed(ActionEvent e)
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866 copy_actionPerformed(null);
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867 delete_actionPerformed(null);
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873 * @param e DOCUMENT ME!
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875 protected void delete_actionPerformed(ActionEvent e)
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878 if (viewport.getSelectionGroup() == null)
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883 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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884 HistoryItem.HIDE));
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886 SequenceGroup sg = viewport.getSelectionGroup();
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887 boolean allSequences = false;
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888 if (sg.sequences.size() == viewport.alignment.getHeight())
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890 allSequences = true;
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893 for (int i = 0; i < sg.sequences.size(); i++)
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895 SequenceI seq = sg.getSequenceAt(i);
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896 int index = viewport.getAlignment().findIndex(seq);
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897 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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899 // If the cut affects all sequences, remove highlighted columns
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902 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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903 sg.getEndRes() + 1);
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906 if (seq.getSequence().length() < 1)
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908 viewport.getAlignment().deleteSequence(seq);
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912 viewport.getAlignment().getSequences().setElementAt(seq, index);
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916 viewport.setSelectionGroup(null);
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917 viewport.alignment.deleteGroup(sg);
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919 viewport.firePropertyChange("alignment", null,
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920 viewport.getAlignment().getSequences());
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924 if (viewport.getAlignment().getHeight() < 1)
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928 this.setClosed(true);
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930 catch (Exception ex)
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939 * @param e DOCUMENT ME!
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941 protected void deleteGroups_actionPerformed(ActionEvent e)
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943 viewport.alignment.deleteAllGroups();
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944 viewport.setSelectionGroup(null);
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945 alignPanel.repaint();
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951 * @param e DOCUMENT ME!
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953 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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955 SequenceGroup sg = new SequenceGroup();
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957 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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960 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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963 sg.setEndRes(viewport.alignment.getWidth() - 1);
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964 viewport.setSelectionGroup(sg);
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965 PaintRefresher.Refresh(null, viewport.alignment);
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971 * @param e DOCUMENT ME!
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973 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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975 viewport.setSelectionGroup(null);
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976 viewport.getColumnSelection().clear();
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977 viewport.setSelectionGroup(null);
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978 alignPanel.annotationPanel.activeRes = null;
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979 PaintRefresher.Refresh(null, viewport.alignment);
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985 * @param e DOCUMENT ME!
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987 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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989 SequenceGroup sg = viewport.getSelectionGroup();
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993 selectAllSequenceMenuItem_actionPerformed(null);
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998 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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1001 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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1004 PaintRefresher.Refresh(null, viewport.alignment);
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1010 * @param e DOCUMENT ME!
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1012 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1014 ColumnSelection colSel = viewport.getColumnSelection();
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1016 if (colSel.size() > 0)
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1018 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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1019 HistoryItem.HIDE));
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1021 int min = colSel.getMin();
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1022 viewport.getAlignment().trimLeft(min);
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1023 colSel.compensateForEdit(0, min);
\r
1025 if (viewport.getSelectionGroup() != null)
\r
1027 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1030 Vector groups = viewport.alignment.getGroups();
\r
1032 for (int i = 0; i < groups.size(); i++)
\r
1034 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1036 if (!sg.adjustForRemoveLeft(min))
\r
1038 viewport.alignment.deleteGroup(sg);
\r
1042 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1049 * @param e DOCUMENT ME!
\r
1051 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1053 ColumnSelection colSel = viewport.getColumnSelection();
\r
1055 if (colSel.size() > 0)
\r
1057 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1058 HistoryItem.HIDE));
\r
1060 int max = colSel.getMax();
\r
1061 viewport.getAlignment().trimRight(max);
\r
1063 if (viewport.getSelectionGroup() != null)
\r
1065 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1068 Vector groups = viewport.alignment.getGroups();
\r
1070 for (int i = 0; i < groups.size(); i++)
\r
1072 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1074 if (!sg.adjustForRemoveRight(max))
\r
1076 viewport.alignment.deleteGroup(sg);
\r
1080 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1087 * @param e DOCUMENT ME!
\r
1089 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1091 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1092 viewport.alignment, HistoryItem.HIDE));
\r
1094 //This is to maintain viewport position on first residue
\r
1095 //of first sequence
\r
1096 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1097 int startRes = seq.findPosition(viewport.startRes);
\r
1099 viewport.getAlignment().removeGaps();
\r
1101 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1103 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1109 * @param e DOCUMENT ME!
\r
1111 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1113 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1114 HistoryItem.HIDE));
\r
1116 //This is to maintain viewport position on first residue
\r
1117 //of first sequence
\r
1118 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1119 int startRes = seq.findPosition(viewport.startRes);
\r
1122 SequenceI current;
\r
1125 Vector seqs = null;
\r
1128 int end = viewport.alignment.getWidth();
\r
1130 if (viewport.getSelectionGroup() != null
\r
1131 && viewport.getSelectionGroup().sequences != null
\r
1132 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1134 seqs = viewport.getSelectionGroup().sequences;
\r
1135 start = viewport.getSelectionGroup().getStartRes();
\r
1136 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1140 seqs = viewport.alignment.getSequences();
\r
1143 for (int i = 0; i < seqs.size(); i++)
\r
1145 current = (SequenceI) seqs.elementAt(i);
\r
1146 jSize = current.getLength();
\r
1148 // Removing a range is much quicker than removing gaps
\r
1149 // one by one for long sequences
\r
1151 int rangeStart=-1, rangeEnd=-1;
\r
1155 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1157 if(rangeStart==-1)
\r
1172 current.deleteChars(rangeStart, rangeEnd);
\r
1173 j-=rangeEnd-rangeStart;
\r
1174 jSize-=rangeEnd-rangeStart;
\r
1182 while (j < end && j < jSize);
\r
1185 current.deleteChars(rangeStart, rangeEnd);
\r
1189 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1191 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1194 public void alignmentChanged()
\r
1196 if(viewport.vconsensus!=null)
\r
1198 viewport.updateConsensus();
\r
1199 viewport.updateConservation();
\r
1201 resetAllColourSchemes();
\r
1202 if(alignPanel.overviewPanel!=null)
\r
1203 alignPanel.overviewPanel.updateOverviewImage();
\r
1205 Provenance prov = viewport.alignment.getProvenance();
\r
1208 prov = new Provenance();
\r
1209 viewport.alignment.setProvenance(prov);
\r
1212 prov.addEntry("Me",
\r
1213 "Edited in Jalview", new java.util.Date(), "myID");
\r
1215 alignPanel.repaint();
\r
1218 void resetAllColourSchemes()
\r
1220 ColourSchemeI cs = viewport.globalColourScheme;
\r
1223 if (cs instanceof ClustalxColourScheme)
\r
1225 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1226 resetClustalX(viewport.alignment.getSequences(),
\r
1227 viewport.alignment.getWidth());
\r
1230 cs.setConsensus(viewport.vconsensus);
\r
1231 if (cs.conservationApplied())
\r
1233 Alignment al = (Alignment) viewport.alignment;
\r
1234 Conservation c = new Conservation("All",
\r
1235 ResidueProperties.propHash, 3,
\r
1236 al.getSequences(), 0,
\r
1237 al.getWidth() - 1);
\r
1239 c.verdict(false, viewport.ConsPercGaps);
\r
1241 cs.setConservation(c);
\r
1245 int s, sSize = viewport.alignment.getGroups().size();
\r
1246 for(s=0; s<sSize; s++)
\r
1248 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1249 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1251 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1253 sg.recalcConservation();
\r
1260 * @param e DOCUMENT ME!
\r
1262 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1264 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1265 HistoryItem.HIDE));
\r
1267 SequenceI current;
\r
1268 int Width = viewport.getAlignment().getWidth();
\r
1270 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1273 current = viewport.getAlignment().getSequenceAt(i);
\r
1275 if (current.getLength() < Width)
\r
1277 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1281 alignmentChanged();
\r
1287 * @param e DOCUMENT ME!
\r
1289 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1291 JInternalFrame frame = new JInternalFrame();
\r
1292 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1293 frame.setContentPane(finder);
\r
1294 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1295 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1301 * @param e DOCUMENT ME!
\r
1303 public void font_actionPerformed(ActionEvent e)
\r
1305 new FontChooser(alignPanel);
\r
1311 * @param e DOCUMENT ME!
\r
1313 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1315 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1317 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1318 alignPanel.repaint();
\r
1321 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1323 viewport.setShowDBPrefix(seqDBRef.isSelected());
\r
1325 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1326 alignPanel.repaint();
\r
1333 * @param e DOCUMENT ME!
\r
1335 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1337 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1338 alignPanel.repaint();
\r
1344 * @param e DOCUMENT ME!
\r
1346 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1348 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1349 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1350 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1351 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1352 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1353 alignPanel.repaint();
\r
1359 * @param e DOCUMENT ME!
\r
1361 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1363 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1364 alignPanel.repaint();
\r
1370 * @param e DOCUMENT ME!
\r
1372 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1374 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1375 alignPanel.repaint();
\r
1381 * @param e DOCUMENT ME!
\r
1383 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1385 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1386 alignPanel.repaint();
\r
1392 * @param e DOCUMENT ME!
\r
1394 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1396 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1397 alignPanel.repaint();
\r
1403 * @param e DOCUMENT ME!
\r
1405 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1407 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1408 alignPanel.repaint();
\r
1414 * @param e DOCUMENT ME!
\r
1416 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1418 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1419 alignPanel.repaint();
\r
1425 * @param evt DOCUMENT ME!
\r
1427 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1429 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1431 if (viewport.showSequenceFeatures &&
\r
1432 ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
\r
1434 System.out.println("new fetcher");
\r
1435 new SequenceFeatureFetcher(viewport.
\r
1440 featureSettings.setEnabled(true);
\r
1442 alignPanel.repaint();
\r
1448 * @param e DOCUMENT ME!
\r
1450 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1452 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1453 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1459 * @param e DOCUMENT ME!
\r
1461 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1463 if (alignPanel.overviewPanel != null)
\r
1468 JInternalFrame frame = new JInternalFrame();
\r
1469 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1470 frame.setContentPane(overview);
\r
1471 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1472 frame.getWidth(), frame.getHeight());
\r
1474 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1475 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1477 public void internalFrameClosed(
\r
1478 javax.swing.event.InternalFrameEvent evt)
\r
1480 alignPanel.setOverviewPanel(null);
\r
1485 alignPanel.setOverviewPanel(overview);
\r
1491 * @param e DOCUMENT ME!
\r
1493 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1495 changeColour(null);
\r
1501 * @param e DOCUMENT ME!
\r
1503 public void clustalColour_actionPerformed(ActionEvent e)
\r
1505 changeColour(new ClustalxColourScheme(
\r
1506 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1512 * @param e DOCUMENT ME!
\r
1514 public void zappoColour_actionPerformed(ActionEvent e)
\r
1516 changeColour(new ZappoColourScheme());
\r
1522 * @param e DOCUMENT ME!
\r
1524 public void taylorColour_actionPerformed(ActionEvent e)
\r
1526 changeColour(new TaylorColourScheme());
\r
1532 * @param e DOCUMENT ME!
\r
1534 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1536 changeColour(new HydrophobicColourScheme());
\r
1542 * @param e DOCUMENT ME!
\r
1544 public void helixColour_actionPerformed(ActionEvent e)
\r
1546 changeColour(new HelixColourScheme());
\r
1552 * @param e DOCUMENT ME!
\r
1554 public void strandColour_actionPerformed(ActionEvent e)
\r
1556 changeColour(new StrandColourScheme());
\r
1562 * @param e DOCUMENT ME!
\r
1564 public void turnColour_actionPerformed(ActionEvent e)
\r
1566 changeColour(new TurnColourScheme());
\r
1572 * @param e DOCUMENT ME!
\r
1574 public void buriedColour_actionPerformed(ActionEvent e)
\r
1576 changeColour(new BuriedColourScheme());
\r
1582 * @param e DOCUMENT ME!
\r
1584 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1586 changeColour(new NucleotideColourScheme());
\r
1592 * @param e DOCUMENT ME!
\r
1594 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1596 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1602 * @param cs DOCUMENT ME!
\r
1604 void changeColour(ColourSchemeI cs)
\r
1606 int threshold = 0;
\r
1610 if (viewport.getAbovePIDThreshold())
\r
1612 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1615 cs.setThreshold(threshold,
\r
1616 viewport.getIgnoreGapsConsensus());
\r
1618 viewport.setGlobalColourScheme(cs);
\r
1622 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1625 if (viewport.getConservationSelected())
\r
1628 Alignment al = (Alignment) viewport.alignment;
\r
1629 Conservation c = new Conservation("All",
\r
1630 ResidueProperties.propHash, 3,
\r
1631 al.getSequences(), 0,
\r
1632 al.getWidth() - 1);
\r
1635 c.verdict(false, viewport.ConsPercGaps);
\r
1637 cs.setConservation(c);
\r
1639 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1644 cs.setConservation(null);
\r
1647 cs.setConsensus(viewport.vconsensus);
\r
1650 viewport.setGlobalColourScheme(cs);
\r
1652 if (viewport.getColourAppliesToAllGroups())
\r
1654 Vector groups = viewport.alignment.getGroups();
\r
1656 for (int i = 0; i < groups.size(); i++)
\r
1658 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1666 if (cs instanceof ClustalxColourScheme)
\r
1668 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1670 else if (cs instanceof UserColourScheme)
\r
1672 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1678 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1680 catch (Exception ex)
\r
1685 if (viewport.getAbovePIDThreshold()
\r
1686 || cs instanceof PIDColourScheme
\r
1687 || cs instanceof Blosum62ColourScheme)
\r
1689 sg.cs.setThreshold(threshold,
\r
1690 viewport.getIgnoreGapsConsensus());
\r
1692 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1696 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1699 if (viewport.getConservationSelected())
\r
1701 Conservation c = new Conservation("Group",
\r
1702 ResidueProperties.propHash, 3,
\r
1704 viewport.alignment.getWidth() - 1);
\r
1706 c.verdict(false, viewport.ConsPercGaps);
\r
1707 sg.cs.setConservation(c);
\r
1710 sg.cs.setConservation(null);
\r
1714 if (alignPanel.getOverviewPanel() != null)
\r
1716 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1719 alignPanel.repaint();
\r
1725 * @param e DOCUMENT ME!
\r
1727 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1729 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1731 SliderPanel.setPIDSliderSource(alignPanel,
\r
1732 viewport.getGlobalColourScheme(),
\r
1734 SliderPanel.showPIDSlider();
\r
1741 * @param e DOCUMENT ME!
\r
1743 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1745 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1747 SliderPanel.setConservationSlider(alignPanel,
\r
1748 viewport.globalColourScheme,
\r
1750 SliderPanel.showConservationSlider();
\r
1757 * @param e DOCUMENT ME!
\r
1759 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1761 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1763 viewport.setAbovePIDThreshold(false);
\r
1764 abovePIDThreshold.setSelected(false);
\r
1766 changeColour(viewport.getGlobalColourScheme());
\r
1768 modifyConservation_actionPerformed(null);
\r
1774 * @param e DOCUMENT ME!
\r
1776 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1778 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1780 conservationMenuItem.setSelected(false);
\r
1781 viewport.setConservationSelected(false);
\r
1783 changeColour(viewport.getGlobalColourScheme());
\r
1785 modifyPID_actionPerformed(null);
\r
1791 * @param e DOCUMENT ME!
\r
1793 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1795 if (e.getActionCommand().equals("User Defined..."))
\r
1797 new UserDefinedColours(alignPanel, null);
\r
1801 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1802 getUserColourSchemes().get(e.getActionCommand());
\r
1804 changeColour(udc);
\r
1808 public void updateUserColourMenu()
\r
1811 Component[] menuItems = colourMenu.getMenuComponents();
\r
1812 int i, iSize = menuItems.length;
\r
1813 for (i = 0; i < iSize; i++)
\r
1815 if (menuItems[i].getName() != null &&
\r
1816 menuItems[i].getName().equals("USER_DEFINED"))
\r
1818 colourMenu.remove(menuItems[i]);
\r
1822 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1824 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1825 getUserColourSchemes().keys();
\r
1827 while (userColours.hasMoreElements())
\r
1829 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1830 nextElement().toString());
\r
1831 radioItem.setName("USER_DEFINED");
\r
1832 radioItem.addMouseListener(new MouseAdapter()
\r
1834 public void mousePressed(MouseEvent evt)
\r
1836 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1838 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1840 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1841 "Remove from default list?",
\r
1842 "Remove user defined colour",
\r
1843 JOptionPane.YES_NO_OPTION);
\r
1844 if(option == JOptionPane.YES_OPTION)
\r
1846 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1847 colourMenu.remove(radioItem);
\r
1850 radioItem.addActionListener(new ActionListener()
\r
1852 public void actionPerformed(ActionEvent evt)
\r
1854 userDefinedColour_actionPerformed(evt);
\r
1860 radioItem.addActionListener(new ActionListener()
\r
1862 public void actionPerformed(ActionEvent evt)
\r
1864 userDefinedColour_actionPerformed(evt);
\r
1868 colourMenu.insert(radioItem, 15);
\r
1869 colours.add(radioItem);
\r
1877 * @param e DOCUMENT ME!
\r
1879 public void PIDColour_actionPerformed(ActionEvent e)
\r
1881 changeColour(new PIDColourScheme());
\r
1887 * @param e DOCUMENT ME!
\r
1889 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1891 changeColour(new Blosum62ColourScheme());
\r
1897 * @param e DOCUMENT ME!
\r
1899 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1901 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1902 HistoryItem.SORT));
\r
1903 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1904 viewport.getAlignment().getSequenceAt(0));
\r
1905 alignPanel.repaint();
\r
1911 * @param e DOCUMENT ME!
\r
1913 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1915 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1916 HistoryItem.SORT));
\r
1917 AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
\r
1918 alignPanel.repaint();
\r
1924 * @param e DOCUMENT ME!
\r
1926 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1928 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1929 HistoryItem.SORT));
\r
1931 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1932 alignPanel.repaint();
\r
1938 * @param e DOCUMENT ME!
\r
1940 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1942 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1943 JInternalFrame frame = new JInternalFrame();
\r
1944 frame.setContentPane(sp);
\r
1945 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1952 * @param e DOCUMENT ME!
\r
1954 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1956 if ( (viewport.getSelectionGroup() == null) ||
\r
1957 (viewport.getSelectionGroup().getSize() < 2))
\r
1959 JOptionPane.showInternalMessageDialog(this,
\r
1960 "You must select at least 2 sequences.",
\r
1961 "Invalid Selection",
\r
1962 JOptionPane.WARNING_MESSAGE);
\r
1966 JInternalFrame frame = new JInternalFrame();
\r
1967 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1968 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1975 * @param e DOCUMENT ME!
\r
1977 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1979 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1980 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1981 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1982 (viewport.getAlignment().getHeight() < 4))
\r
1984 JOptionPane.showInternalMessageDialog(this,
\r
1985 "Principal component analysis must take\n" +
\r
1986 "at least 4 input sequences.",
\r
1987 "Sequence selection insufficient",
\r
1988 JOptionPane.WARNING_MESSAGE);
\r
1993 new PCAPanel(viewport);
\r
1999 * @param e DOCUMENT ME!
\r
2001 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
2003 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2009 * @param e DOCUMENT ME!
\r
2011 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
2013 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2019 * @param e DOCUMENT ME!
\r
2021 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2023 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2029 * @param e DOCUMENT ME!
\r
2031 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2033 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2039 * @param type DOCUMENT ME!
\r
2040 * @param pwType DOCUMENT ME!
\r
2041 * @param title DOCUMENT ME!
\r
2043 void NewTreePanel(String type, String pwType, String title)
\r
2045 final TreePanel tp;
\r
2047 if ( (viewport.getSelectionGroup() != null) &&
\r
2048 (viewport.getSelectionGroup().getSize() > 3))
\r
2051 SequenceGroup sg = viewport.getSelectionGroup();
\r
2053 /* Decide if the selection is a column region */
\r
2054 while (s < sg.sequences.size())
\r
2056 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2059 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2060 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2061 "Try using the Pad function in the edit menu,\n" +
\r
2062 "or one of the multiple sequence alignment web services.",
\r
2063 "Sequences in selection are not aligned",
\r
2064 JOptionPane.WARNING_MESSAGE);
\r
2070 title = title + " on region";
\r
2071 tp = new TreePanel(viewport,
\r
2072 viewport.getSelectionGroup().sequences, type, pwType,
\r
2073 sg.getStartRes(), sg.getEndRes());
\r
2077 //are the sequences aligned?
\r
2078 if (!viewport.alignment.isAligned())
\r
2080 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2081 "The sequences must be aligned before creating a tree.\n" +
\r
2082 "Try using the Pad function in the edit menu,\n" +
\r
2083 "or one of the multiple sequence alignment web services.",
\r
2084 "Sequences not aligned",
\r
2085 JOptionPane.WARNING_MESSAGE);
\r
2090 tp = new TreePanel(viewport,
\r
2091 viewport.getAlignment().getSequences(), type, pwType,
\r
2093 viewport.alignment.getWidth());
\r
2096 addTreeMenuItem(tp, title);
\r
2097 viewport.setCurrentTree(tp.getTree());
\r
2099 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2105 * @param title DOCUMENT ME!
\r
2106 * @param order DOCUMENT ME!
\r
2108 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2110 final JMenuItem item = new JMenuItem("by " + title);
\r
2112 item.addActionListener(new java.awt.event.ActionListener()
\r
2114 public void actionPerformed(ActionEvent e)
\r
2116 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2117 HistoryItem.SORT));
\r
2119 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2120 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2121 alignPanel.repaint();
\r
2127 * Maintain the Order by->Displayed Tree menu.
\r
2128 * Creates a new menu item for a TreePanel with an appropriate
\r
2129 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2130 * to remove the menu item when the treePanel is closed, and adjust
\r
2131 * the tree leaf to sequence mapping when the alignment is modified.
\r
2132 * @param treePanel Displayed tree window.
\r
2133 * @param title SortBy menu item title.
\r
2135 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2137 final JMenuItem item = new JMenuItem(title);
\r
2141 if (treeCount == 1)
\r
2143 sort.add(sortByTreeMenu);
\r
2146 sortByTreeMenu.add(item);
\r
2147 item.addActionListener(new java.awt.event.ActionListener()
\r
2149 public void actionPerformed(ActionEvent e)
\r
2151 addHistoryItem(new HistoryItem("Tree Sort",
\r
2152 viewport.alignment, HistoryItem.SORT));
\r
2153 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2154 treePanel.getTree());
\r
2155 alignPanel.repaint();
\r
2159 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2160 InternalFrameAdapter()
\r
2162 public void internalFrameClosed(
\r
2163 javax.swing.event.InternalFrameEvent evt)
\r
2166 sortByTreeMenu.remove(item);
\r
2168 if (treeCount == 0)
\r
2170 sort.remove(sortByTreeMenu);
\r
2178 * Work out whether the whole set of sequences
\r
2179 * or just the selected set will be submitted for multiple alignment.
\r
2182 private SequenceI[] gatherSequencesForAlignment()
\r
2184 // Now, check we have enough sequences
\r
2185 SequenceI[] msa = null;
\r
2187 if ( (viewport.getSelectionGroup() != null) &&
\r
2188 (viewport.getSelectionGroup().getSize() > 1))
\r
2190 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2191 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2193 msa = new SequenceI[sz = seqs.getSize()];
\r
2195 for (int i = 0; i < sz; i++)
\r
2197 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2202 Vector seqs = viewport.getAlignment().getSequences();
\r
2204 if (seqs.size() > 1)
\r
2206 msa = new SequenceI[seqs.size()];
\r
2208 for (int i = 0; i < seqs.size(); i++)
\r
2210 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2218 * Decides what is submitted to a secondary structure prediction service,
\r
2219 * the currently selected sequence, or the currently selected alignment
\r
2220 * (where the first sequence in the set is the one that the prediction
\r
2223 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2225 SequenceI seq = null;
\r
2226 SequenceI[] msa = null;
\r
2228 if ( (viewport.getSelectionGroup() != null) &&
\r
2229 (viewport.getSelectionGroup().getSize() > 0))
\r
2231 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2232 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2234 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2236 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2241 msa = new SequenceI[sz = seqs.getSize()];
\r
2243 for (int i = 0; i < sz; i++)
\r
2245 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2251 Vector seqs = viewport.getAlignment().getSequences();
\r
2253 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2255 seq = (SequenceI) seqs.elementAt(0);
\r
2259 msa = new SequenceI[seqs.size()];
\r
2261 for (int i = 0; i < seqs.size(); i++)
\r
2263 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2275 return new SequenceI[]
\r
2285 * @param e DOCUMENT ME!
\r
2287 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2289 // Pick the tree file
\r
2290 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2292 "LAST_DIRECTORY"));
\r
2293 chooser.setFileView(new JalviewFileView());
\r
2294 chooser.setDialogTitle("Select a newick-like tree file");
\r
2295 chooser.setToolTipText("Load a tree file");
\r
2297 int value = chooser.showOpenDialog(null);
\r
2299 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2301 String choice = chooser.getSelectedFile().getPath();
\r
2302 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2306 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2308 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2310 catch (Exception ex)
\r
2312 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2313 "Problem reading tree file",
\r
2315 JOptionPane.WARNING_MESSAGE);
\r
2316 ex.printStackTrace();
\r
2322 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2324 return ShowNewickTree(nf,title,600,500,4,5);
\r
2329 * @param nf DOCUMENT ME!
\r
2330 * @param title DOCUMENT ME!
\r
2332 * @return DOCUMENT ME!
\r
2334 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2336 TreePanel tp = null;
\r
2342 if (nf.getTree() != null)
\r
2344 tp = new TreePanel(viewport,
\r
2345 viewport.getAlignment().getSequences(), nf,
\r
2352 tp.setLocation(x,y);
\r
2355 Desktop.addInternalFrame(tp, title, w, h);
\r
2356 addTreeMenuItem(tp, title);
\r
2359 catch (Exception ex)
\r
2361 ex.printStackTrace();
\r
2372 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2373 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2374 printJob.setPrintable(alignPanel, pf);
\r
2376 if (printJob.printDialog())
\r
2382 catch (Exception PrintException)
\r
2384 PrintException.printStackTrace();
\r
2391 * Generates menu items and listener event actions for web service clients
\r
2394 public void BuildWebServiceMenu()
\r
2396 if ( (Discoverer.services != null)
\r
2397 && (Discoverer.services.size() > 0))
\r
2399 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2400 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2401 Vector wsmenu = new Vector();
\r
2402 if (msaws != null)
\r
2404 // Add any Multiple Sequence Alignment Services
\r
2405 final JMenu msawsmenu = new JMenu("Alignment");
\r
2406 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2408 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2410 final JMenuItem method = new JMenuItem(sh.getName());
\r
2411 method.addActionListener(new ActionListener()
\r
2413 public void actionPerformed(ActionEvent e)
\r
2415 SequenceI[] msa = gatherSequencesForAlignment();
\r
2416 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2417 false, true, viewport.getAlignment().getDataset());
\r
2422 msawsmenu.add(method);
\r
2423 // Deal with services that we know accept partial alignments.
\r
2424 if (sh.getName().indexOf("lustal") > -1)
\r
2426 // We know that ClustalWS can accept partial alignments for refinement.
\r
2427 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2428 methodR.addActionListener(new ActionListener()
\r
2430 public void actionPerformed(ActionEvent e)
\r
2432 SequenceI[] msa = gatherSequencesForAlignment();
\r
2433 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2434 true, true, viewport.getAlignment().getDataset());
\r
2439 msawsmenu.add(methodR);
\r
2443 wsmenu.add(msawsmenu);
\r
2445 if (secstrpr != null)
\r
2447 // Add any secondary structure prediction services
\r
2448 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2449 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2451 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2453 final JMenuItem method = new JMenuItem(sh.getName());
\r
2454 method.addActionListener(new ActionListener()
\r
2456 public void actionPerformed(ActionEvent e)
\r
2458 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2459 if (msa.length == 1)
\r
2461 // Single Sequence prediction
\r
2462 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2466 if (msa.length > 1)
\r
2468 // Single Sequence prediction
\r
2469 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2475 secstrmenu.add(method);
\r
2477 wsmenu.add(secstrmenu);
\r
2479 this.webService.removeAll();
\r
2480 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2482 webService.add( (JMenu) wsmenu.get(i));
\r
2487 this.webService.removeAll();
\r
2488 this.webService.add(this.webServiceNoServices);
\r
2490 // TODO: add in rediscovery function
\r
2491 // TODO: reduce code redundancy.
\r
2492 // TODO: group services by location as well as function.
\r
2495 public void vamsasStore_actionPerformed(ActionEvent e)
\r
2497 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2498 getProperty("LAST_DIRECTORY"));
\r
2500 chooser.setFileView(new JalviewFileView());
\r
2501 chooser.setDialogTitle("Export to Vamsas file");
\r
2502 chooser.setToolTipText("Export");
\r
2504 int value = chooser.showSaveDialog(this);
\r
2506 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2508 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2509 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
2510 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
2514 public void featureSettings_actionPerformed(ActionEvent e)
\r
2516 new FeatureSettings(viewport, alignPanel);
\r
2521 public void showTranslation_actionPerformed(ActionEvent e)
\r
2523 int s, sSize = viewport.alignment.getHeight();
\r
2524 SequenceI [] newSeq = new SequenceI[sSize];
\r
2527 StringBuffer protein;
\r
2529 for(s=0; s<sSize; s++)
\r
2531 protein = new StringBuffer();
\r
2532 seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
\r
2533 resSize = seq.length();
\r
2534 for(res = 0; res < resSize; res+=3)
\r
2536 String codon = seq.substring(res, res+3);
\r
2537 codon = codon.replace('U', 'T');
\r
2538 String aa = ResidueProperties.codonTranslate(codon);
\r
2540 protein.append(viewport.getGapCharacter());
\r
2541 else if(aa.equals("STOP"))
\r
2542 protein.append("X");
\r
2544 protein.append( aa );
\r
2546 newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
\r
2550 AlignmentI al = new Alignment(newSeq);
\r
2551 al.setDataset(null);
\r
2554 ////////////////////////////////
\r
2555 // Copy annotations across
\r
2556 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2557 = viewport.alignment.getAlignmentAnnotation();
\r
2559 for (int i = 0; i < annotations.length; i++)
\r
2562 if (annotations[i].label.equals("Quality") ||
\r
2563 annotations[i].label.equals("Conservation") ||
\r
2564 annotations[i].label.equals("Consensus"))
\r
2570 aSize = viewport.alignment.getWidth()/3;
\r
2571 jalview.datamodel.Annotation [] anots =
\r
2572 new jalview.datamodel.Annotation[aSize];
\r
2574 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2576 if( annotations[i].annotations[a]==null
\r
2577 || annotations[i].annotations[a]==null)
\r
2580 anots[a/3] = new Annotation(
\r
2581 annotations[i].annotations[a].displayCharacter,
\r
2582 annotations[i].annotations[a].description,
\r
2583 annotations[i].annotations[a].secondaryStructure,
\r
2584 annotations[i].annotations[a].value,
\r
2585 annotations[i].annotations[a].colour);
\r
2588 jalview.datamodel.AlignmentAnnotation aa
\r
2589 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2590 annotations[i].description, anots );
\r
2591 al.addAnnotation(aa);
\r
2595 AlignFrame af = new AlignFrame(al);
\r
2596 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2598 NEW_WINDOW_HEIGHT);
\r
2601 // AlignViewport newViewport = new AlignViewport(al);
\r
2602 // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2603 // tabbedPane.add("Protein", ap);
\r
2604 // viewports.add(newViewport);
\r
2605 // alignPanels.add(ap);
\r
2608 /////////////////////////
\r
2610 // AlignViewport ds = new AlignViewport(al.getDataset());
\r
2611 // ds.setDataset(true);
\r
2612 // AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2613 // tabbedPane.add("Dataset", dap);
\r
2614 // viewports.add(ds);
\r
2615 // alignPanels.add(dap);
\r
2616 /////////////////////////
\r
2621 /*public void tabSelected()
\r
2623 int index = tabbedPane.getSelectedIndex();
\r
2624 viewport = (AlignViewport)viewports.elementAt(index);
\r
2625 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r