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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42 * @version $Revision$
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44 public class AlignFrame
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45 extends GAlignFrame implements ClipboardOwner
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47 /** DOCUMENT ME!! */
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48 public static final int NEW_WINDOW_WIDTH = 700;
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50 /** DOCUMENT ME!! */
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51 public static final int NEW_WINDOW_HEIGHT = 500;
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52 AlignmentPanel alignPanel;
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53 AlignViewport viewport;
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55 Vector viewports = new Vector();
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56 Vector alignPanels = new Vector();
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58 /** DOCUMENT ME!! */
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59 public String currentFileFormat = null;
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60 Stack historyList = new Stack();
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61 Stack redoList = new Stack();
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62 private int treeCount = 0;
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66 * Creates a new AlignFrame object.
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68 * @param al DOCUMENT ME!
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70 public AlignFrame(AlignmentI al)
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72 viewport = new AlignViewport(al);
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73 viewports.add(viewport);
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76 if(viewport.vconsensus==null)
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78 //Out of memory calculating consensus.
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79 BLOSUM62Colour.setEnabled(false);
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80 PIDColour.setEnabled(false);
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81 conservationMenuItem.setEnabled(false);
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82 modifyConservation.setEnabled(false);
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83 abovePIDThreshold.setEnabled(false);
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84 modifyPID.setEnabled(false);
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87 alignPanel = new AlignmentPanel(this, viewport);
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88 alignPanels.add(alignPanel);
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90 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
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92 if(sortby.equals("Id"))
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93 sortIDMenuItem_actionPerformed(null);
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94 else if(sortby.equals("Pairwise Identity"))
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95 sortPairwiseMenuItem_actionPerformed(null);
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97 tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
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100 /////////////////////////
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102 if(al.getDataset()==null)
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104 al.setDataset(null);
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107 AlignViewport ds = new AlignViewport(al.getDataset(), true);
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108 AlignmentPanel dap = new AlignmentPanel(this, ds);
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109 tabbedPane.add("Dataset", dap);
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111 alignPanels.add(dap);
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112 /////////////////////////
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115 viewport.addPropertyChangeListener(new PropertyChangeListener()
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117 public void propertyChange(PropertyChangeEvent evt)
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119 if (evt.getPropertyName().equals("alignment"))
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121 alignmentChanged();
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127 if(Desktop.desktop!=null)
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128 addServiceListeners();
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131 /* Set up intrinsic listeners for dynamically generated GUI bits. */
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132 private void addServiceListeners()
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134 final java.beans.PropertyChangeListener thisListener;
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135 // Do this once to get current state
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136 BuildWebServiceMenu();
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137 Desktop.discoverer.addPropertyChangeListener(
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138 thisListener = new java.beans.PropertyChangeListener()
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140 public void propertyChange(PropertyChangeEvent evt)
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142 // System.out.println("Discoverer property change.");
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143 if (evt.getPropertyName().equals("services"))
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145 // System.out.println("Rebuilding web service menu");
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146 BuildWebServiceMenu();
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150 addInternalFrameListener(new javax.swing.event.
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151 InternalFrameAdapter()
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153 public void internalFrameClosed(
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154 javax.swing.event.InternalFrameEvent evt)
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156 // System.out.println("deregistering discoverer listener");
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157 Desktop.discoverer.removePropertyChangeListener(thisListener);
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158 closeMenuItem_actionPerformed(null);
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165 public AlignViewport getViewport()
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172 Added so Castor Mapping file can obtain Jalview Version
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174 public String getVersion()
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176 return jalview.bin.Cache.getProperty("VERSION");
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183 * @param String DOCUMENT ME!
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186 public void parseGroupsFile(String file)
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190 BufferedReader in = new BufferedReader(new FileReader(file));
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191 SequenceI seq = null;
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192 String line, type, desc, token;
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194 int index, start, end;
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195 StringTokenizer st;
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196 SequenceFeature sf;
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197 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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199 while ( (line = in.readLine()) != null)
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202 st = new StringTokenizer(line, "\t");
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203 if (st.countTokens() == 2)
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205 type = st.nextToken();
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206 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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207 fr.setColour(type, ucs.findColour("A"));
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211 while (st.hasMoreElements())
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213 desc = st.nextToken();
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214 token = st.nextToken();
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215 if (!token.equals("ID_NOT_SPECIFIED"))
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217 index = viewport.alignment.findIndex(viewport.alignment.findName(
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223 index = Integer.parseInt(st.nextToken());
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226 start = Integer.parseInt(st.nextToken());
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227 end = Integer.parseInt(st.nextToken());
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229 seq = viewport.alignment.getSequenceAt(index);
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230 start = seq.findIndex(start) - 1;
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231 end = seq.findIndex(end) - 1;
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233 type = st.nextToken();
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235 if (fr.getColour(type) == null)
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237 // Probably the old style groups file
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238 UserColourScheme ucs = new UserColourScheme(type);
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239 fr.setColour(type, ucs.findColour("A"));
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243 sf = new SequenceFeature(type, desc, "", start, end);
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245 seq.addSequenceFeature(sf);
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248 // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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249 // sg.addSequence(seq, false);
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251 // viewport.alignment.addGroup(sg);
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256 viewport.showSequenceFeatures = true;
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257 ((Alignment)viewport.alignment).featuresAdded = true;
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259 alignPanel.repaint();
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262 catch (Exception ex)
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264 System.out.println("Error parsing groups file: " + ex);
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271 * @param e DOCUMENT ME!
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273 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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275 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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280 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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285 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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286 }, currentFileFormat);
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288 chooser.setAcceptAllFileFilterUsed(false);
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289 chooser.setFileView(new JalviewFileView());
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290 chooser.setDialogTitle("Save Alignment to file");
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291 chooser.setToolTipText("Save");
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293 int value = chooser.showSaveDialog(this);
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295 if (value == JalviewFileChooser.APPROVE_OPTION)
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297 currentFileFormat = chooser.getSelectedFormat();
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299 if (currentFileFormat == null)
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301 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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302 "You must select a file format before saving!",
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303 "File format not specified",
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304 JOptionPane.WARNING_MESSAGE);
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305 value = chooser.showSaveDialog(this);
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309 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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310 currentFileFormat);
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312 String choice = chooser.getSelectedFile().getPath();
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313 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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315 saveAlignment(choice, currentFileFormat);
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319 public boolean saveAlignment(String file, String format)
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321 if (format.equalsIgnoreCase("Jalview"))
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323 String shortName = title;
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325 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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327 shortName = shortName.substring(shortName.lastIndexOf(
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328 java.io.File.separatorChar) + 1);
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331 Jalview2XML.SaveAlignment(this, file, shortName);
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333 // USE Jalview2XML to save this file
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338 String output = new FormatAdapter().formatSequences(format,
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339 viewport.getAlignment().
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341 if (output == null)
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348 java.io.PrintWriter out = new java.io.PrintWriter(
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349 new java.io.FileWriter(file));
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355 catch (Exception ex)
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357 ex.printStackTrace();
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366 * @param e DOCUMENT ME!
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368 protected void outputText_actionPerformed(ActionEvent e)
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370 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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371 Desktop.addInternalFrame(cap,
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372 "Alignment output - " + e.getActionCommand(), 600,
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374 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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375 viewport.getAlignment().
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382 * @param e DOCUMENT ME!
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384 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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386 new HTMLOutput(viewport);
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389 public void createImageMap(File file, String image)
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391 alignPanel.makePNGImageMap(file, image);
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397 * @param e DOCUMENT ME!
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399 public void createPNG(File f)
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401 alignPanel.makePNG(f);
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407 * @param e DOCUMENT ME!
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409 public void createEPS(File f)
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411 alignPanel.makeEPS(f);
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417 * @param e DOCUMENT ME!
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419 public void printMenuItem_actionPerformed(ActionEvent e)
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421 //Putting in a thread avoids Swing painting problems
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422 PrintThread thread = new PrintThread();
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429 * @param e DOCUMENT ME!
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431 public void closeMenuItem_actionPerformed(ActionEvent e)
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435 PaintRefresher.components.remove(viewport.alignment);
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436 this.setClosed(true);
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438 catch (Exception ex)
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446 void updateEditMenuBar()
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448 if (historyList.size() > 0)
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450 undoMenuItem.setEnabled(true);
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452 HistoryItem hi = (HistoryItem) historyList.peek();
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453 undoMenuItem.setText("Undo " + hi.getDescription());
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457 undoMenuItem.setEnabled(false);
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458 undoMenuItem.setText("Undo");
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461 if (redoList.size() > 0)
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463 redoMenuItem.setEnabled(true);
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465 HistoryItem hi = (HistoryItem) redoList.peek();
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466 redoMenuItem.setText("Redo " + hi.getDescription());
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470 redoMenuItem.setEnabled(false);
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471 redoMenuItem.setText("Redo");
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478 * @param hi DOCUMENT ME!
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480 public void addHistoryItem(HistoryItem hi)
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482 historyList.push(hi);
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483 updateEditMenuBar();
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489 * @param e DOCUMENT ME!
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491 protected void undoMenuItem_actionPerformed(ActionEvent e)
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493 HistoryItem hi = (HistoryItem) historyList.pop();
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494 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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495 HistoryItem.HIDE));
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496 restoreHistoryItem(hi);
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497 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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503 * @param e DOCUMENT ME!
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505 protected void redoMenuItem_actionPerformed(ActionEvent e)
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507 HistoryItem hi = (HistoryItem) redoList.pop();
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508 restoreHistoryItem(hi);
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509 updateEditMenuBar();
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510 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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513 // used by undo and redo
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514 void restoreHistoryItem(HistoryItem hi)
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516 if (hi.getType() == HistoryItem.SORT)
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518 for (int i = 0; i < hi.getSequences().size(); i++)
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520 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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527 for (int i = 0; i < hi.getSequences().size(); i++)
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529 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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531 if (restore.getLength() == 0)
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533 restore.setSequence(hi.getHidden().elementAt(i).toString());
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534 viewport.alignment.getSequences().insertElementAt(restore,
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535 hi.getAlignIndex(i));
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539 restore.setSequence(hi.getHidden().elementAt(i).toString());
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543 if (hi.getType() == HistoryItem.PASTE)
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545 for (int i = viewport.alignment.getHeight() - 1;
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546 i > (hi.getSequences().size() - 1); i--)
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548 viewport.alignment.deleteSequence(i);
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553 updateEditMenuBar();
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555 viewport.firePropertyChange("alignment", null,
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556 viewport.getAlignment().getSequences());
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562 * @param up DOCUMENT ME!
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564 public void moveSelectedSequences(boolean up)
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566 SequenceGroup sg = viewport.getSelectionGroup();
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575 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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577 SequenceI seq = viewport.alignment.getSequenceAt(i);
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579 if (!sg.sequences.contains(seq))
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584 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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586 if (sg.sequences.contains(temp))
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591 viewport.alignment.getSequences().setElementAt(temp, i);
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592 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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597 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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599 SequenceI seq = viewport.alignment.getSequenceAt(i);
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601 if (!sg.sequences.contains(seq))
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606 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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608 if (sg.sequences.contains(temp))
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613 viewport.alignment.getSequences().setElementAt(temp, i);
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614 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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618 alignPanel.repaint();
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621 public void lostOwnership(Clipboard clipboard, Transferable contents)
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623 Desktop.jalviewClipboard = null;
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630 * @param e DOCUMENT ME!
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632 protected void copy_actionPerformed(ActionEvent e)
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634 if (viewport.getSelectionGroup() == null)
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639 SequenceGroup sg = viewport.getSelectionGroup();
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641 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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643 Hashtable orderedSeqs = new Hashtable();
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644 SequenceI[] seqs = new SequenceI[sg.getSize()];
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646 for (int i = 0; i < sg.getSize(); i++)
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648 SequenceI seq = sg.getSequenceAt(i);
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649 int index = viewport.alignment.findIndex(seq);
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650 orderedSeqs.put(index + "", seq);
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653 int index = 0, startRes, endRes;
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656 for (int i = 0; i < sg.getSize(); i++)
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658 SequenceI seq = null;
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660 while (seq == null)
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662 if (orderedSeqs.containsKey(index + ""))
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664 seq = (SequenceI) orderedSeqs.get(index + "");
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676 //Returns residue following index if gap
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677 startRes = seq.findPosition(sg.getStartRes());
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680 //Need to find the residue preceeding index if gap
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683 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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685 ch = seq.getCharAt(j);
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686 if (!jalview.util.Comparison.isGap( (ch)))
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694 endRes += seq.getStart() - 1;
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697 seqs[i] = new Sequence(seq.getName(),
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698 seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
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701 seqs[i].setDescription(seq.getDescription());
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702 seqs[i].setDBRef(seq.getDBRef());
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703 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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704 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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708 FastaFile ff = new FastaFile();
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709 ff.addDBPrefix( viewport.showDBPrefix );
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710 ff.addJVSuffix( viewport.showJVSuffix );
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711 c.setContents(new StringSelection( ff.print(seqs)), this);
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712 Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};
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718 * @param e DOCUMENT ME!
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720 protected void pasteNew_actionPerformed(ActionEvent e)
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728 * @param e DOCUMENT ME!
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730 protected void pasteThis_actionPerformed(ActionEvent e)
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732 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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733 HistoryItem.PASTE));
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740 * @param newAlignment DOCUMENT ME!
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742 void paste(boolean newAlignment)
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746 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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747 Transferable contents = c.getContents(this);
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749 if (contents == null)
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754 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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758 String format = IdentifyFile.Identify(str, "Paste");
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759 SequenceI[] sequences;
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761 if(Desktop.jalviewClipboard!=null)
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763 // The clipboard was filled from within Jalview, we must use the sequences
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764 // And dataset from the copied alignment
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765 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
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769 sequences = new FormatAdapter().readFile(str, "Paste", format);
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775 Alignment alignment = new Alignment(sequences);
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777 if(Desktop.jalviewClipboard!=null)
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778 alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
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780 alignment.setDataset( null );
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783 AlignFrame af = new AlignFrame(alignment);
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784 String newtitle = new String("Copied sequences");
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786 if (title.startsWith("Copied sequences"))
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792 newtitle = newtitle.concat("- from " + title);
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795 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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796 NEW_WINDOW_HEIGHT);
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801 for (int i = 0; i < sequences.length; i++)
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803 viewport.alignment.addSequence(sequences[i]);
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804 if(sequences[i].getDatasetSequence()==null)
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806 ////////////////////////////
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807 //Datset needs extension;
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808 /////////////////////////////
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809 Sequence ds = new Sequence(sequences[i].getName(),
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810 AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
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811 sequences[i].getStart(),
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812 sequences[i].getEnd());
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813 sequences[i].setDatasetSequence(ds);
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814 viewport.alignment.getDataset().addSequence(ds);
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820 viewport.setEndSeq(viewport.alignment.getHeight());
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821 viewport.alignment.getWidth();
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822 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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825 catch (Exception ex)
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827 // could be anything being pasted in here
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836 * @param e DOCUMENT ME!
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838 protected void cut_actionPerformed(ActionEvent e)
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840 copy_actionPerformed(null);
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841 delete_actionPerformed(null);
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847 * @param e DOCUMENT ME!
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849 protected void delete_actionPerformed(ActionEvent e)
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852 if (viewport.getSelectionGroup() == null)
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857 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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858 HistoryItem.HIDE));
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860 SequenceGroup sg = viewport.getSelectionGroup();
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861 boolean allSequences = false;
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862 if (sg.sequences.size() == viewport.alignment.getHeight())
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864 allSequences = true;
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867 for (int i = 0; i < sg.sequences.size(); i++)
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869 SequenceI seq = sg.getSequenceAt(i);
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870 int index = viewport.getAlignment().findIndex(seq);
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871 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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873 // If the cut affects all sequences, remove highlighted columns
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876 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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877 sg.getEndRes() + 1);
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880 if (seq.getSequence().length() < 1)
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882 viewport.getAlignment().deleteSequence(seq);
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886 viewport.getAlignment().getSequences().setElementAt(seq, index);
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890 viewport.setSelectionGroup(null);
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891 viewport.alignment.deleteGroup(sg);
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893 viewport.firePropertyChange("alignment", null,
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894 viewport.getAlignment().getSequences());
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898 if (viewport.getAlignment().getHeight() < 1)
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902 this.setClosed(true);
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904 catch (Exception ex)
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913 * @param e DOCUMENT ME!
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915 protected void deleteGroups_actionPerformed(ActionEvent e)
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917 viewport.alignment.deleteAllGroups();
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918 viewport.setSelectionGroup(null);
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919 alignPanel.repaint();
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925 * @param e DOCUMENT ME!
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927 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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929 SequenceGroup sg = new SequenceGroup();
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931 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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934 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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937 sg.setEndRes(viewport.alignment.getWidth() - 1);
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938 viewport.setSelectionGroup(sg);
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939 PaintRefresher.Refresh(null, viewport.alignment);
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945 * @param e DOCUMENT ME!
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947 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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949 viewport.setSelectionGroup(null);
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950 viewport.getColumnSelection().clear();
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951 viewport.setSelectionGroup(null);
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952 alignPanel.annotationPanel.activeRes = null;
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953 PaintRefresher.Refresh(null, viewport.alignment);
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959 * @param e DOCUMENT ME!
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961 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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963 SequenceGroup sg = viewport.getSelectionGroup();
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967 selectAllSequenceMenuItem_actionPerformed(null);
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972 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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975 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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978 PaintRefresher.Refresh(null, viewport.alignment);
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984 * @param e DOCUMENT ME!
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986 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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988 ColumnSelection colSel = viewport.getColumnSelection();
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990 if (colSel.size() > 0)
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992 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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993 HistoryItem.HIDE));
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995 int min = colSel.getMin();
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996 viewport.getAlignment().trimLeft(min);
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997 colSel.compensateForEdit(0, min);
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999 if (viewport.getSelectionGroup() != null)
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1001 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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1004 Vector groups = viewport.alignment.getGroups();
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1006 for (int i = 0; i < groups.size(); i++)
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1008 SequenceGroup sg = (SequenceGroup) groups.get(i);
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1010 if (!sg.adjustForRemoveLeft(min))
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1012 viewport.alignment.deleteGroup(sg);
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1016 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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1023 * @param e DOCUMENT ME!
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1025 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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1027 ColumnSelection colSel = viewport.getColumnSelection();
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1029 if (colSel.size() > 0)
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1031 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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1032 HistoryItem.HIDE));
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1034 int max = colSel.getMax();
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1035 viewport.getAlignment().trimRight(max);
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1037 if (viewport.getSelectionGroup() != null)
\r
1039 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1042 Vector groups = viewport.alignment.getGroups();
\r
1044 for (int i = 0; i < groups.size(); i++)
\r
1046 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1048 if (!sg.adjustForRemoveRight(max))
\r
1050 viewport.alignment.deleteGroup(sg);
\r
1054 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1061 * @param e DOCUMENT ME!
\r
1063 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1065 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1066 viewport.alignment, HistoryItem.HIDE));
\r
1068 //This is to maintain viewport position on first residue
\r
1069 //of first sequence
\r
1070 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1071 int startRes = seq.findPosition(viewport.startRes);
\r
1073 viewport.getAlignment().removeGaps();
\r
1075 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1077 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1083 * @param e DOCUMENT ME!
\r
1085 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1087 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1088 HistoryItem.HIDE));
\r
1090 //This is to maintain viewport position on first residue
\r
1091 //of first sequence
\r
1092 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1093 int startRes = seq.findPosition(viewport.startRes);
\r
1096 SequenceI current;
\r
1099 Vector seqs = null;
\r
1102 int end = viewport.alignment.getWidth();
\r
1104 if (viewport.getSelectionGroup() != null
\r
1105 && viewport.getSelectionGroup().sequences != null
\r
1106 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1108 seqs = viewport.getSelectionGroup().sequences;
\r
1109 start = viewport.getSelectionGroup().getStartRes();
\r
1110 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1114 seqs = viewport.alignment.getSequences();
\r
1117 for (int i = 0; i < seqs.size(); i++)
\r
1119 current = (SequenceI) seqs.elementAt(i);
\r
1120 jSize = current.getLength();
\r
1122 // Removing a range is much quicker than removing gaps
\r
1123 // one by one for long sequences
\r
1125 int rangeStart=-1, rangeEnd=-1;
\r
1129 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1131 if(rangeStart==-1)
\r
1146 current.deleteChars(rangeStart, rangeEnd);
\r
1147 j-=rangeEnd-rangeStart;
\r
1148 jSize-=rangeEnd-rangeStart;
\r
1156 while (j < end && j < jSize);
\r
1159 current.deleteChars(rangeStart, rangeEnd);
\r
1163 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1165 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1168 public void alignmentChanged()
\r
1170 if(viewport.vconsensus!=null)
\r
1172 viewport.updateConsensus();
\r
1173 viewport.updateConservation();
\r
1175 resetAllColourSchemes();
\r
1176 if(alignPanel.overviewPanel!=null)
\r
1177 alignPanel.overviewPanel.updateOverviewImage();
\r
1179 Provenance prov = viewport.alignment.getProvenance();
\r
1182 prov = new Provenance();
\r
1183 viewport.alignment.setProvenance(prov);
\r
1186 prov.addEntry("Me",
\r
1187 "Edited in Jalview", new java.util.Date(), "myID");
\r
1189 alignPanel.repaint();
\r
1192 void resetAllColourSchemes()
\r
1194 ColourSchemeI cs = viewport.globalColourScheme;
\r
1197 if (cs instanceof ClustalxColourScheme)
\r
1199 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1200 resetClustalX(viewport.alignment.getSequences(),
\r
1201 viewport.alignment.getWidth());
\r
1204 cs.setConsensus(viewport.vconsensus);
\r
1205 if (cs.conservationApplied())
\r
1207 Alignment al = (Alignment) viewport.alignment;
\r
1208 Conservation c = new Conservation("All",
\r
1209 ResidueProperties.propHash, 3,
\r
1210 al.getSequences(), 0,
\r
1211 al.getWidth() - 1);
\r
1213 c.verdict(false, viewport.ConsPercGaps);
\r
1215 cs.setConservation(c);
\r
1219 int s, sSize = viewport.alignment.getGroups().size();
\r
1220 for(s=0; s<sSize; s++)
\r
1222 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1223 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1225 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1227 sg.recalcConservation();
\r
1234 * @param e DOCUMENT ME!
\r
1236 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1238 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1239 HistoryItem.HIDE));
\r
1241 SequenceI current;
\r
1242 int Width = viewport.getAlignment().getWidth();
\r
1244 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1247 current = viewport.getAlignment().getSequenceAt(i);
\r
1249 if (current.getLength() < Width)
\r
1251 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1255 alignmentChanged();
\r
1261 * @param e DOCUMENT ME!
\r
1263 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1265 JInternalFrame frame = new JInternalFrame();
\r
1266 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1267 frame.setContentPane(finder);
\r
1268 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1269 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1275 * @param e DOCUMENT ME!
\r
1277 public void font_actionPerformed(ActionEvent e)
\r
1279 new FontChooser(alignPanel);
\r
1285 * @param e DOCUMENT ME!
\r
1287 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1289 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1291 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1292 alignPanel.repaint();
\r
1295 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1297 viewport.setShowDBPrefix(seqDBRef.isSelected());
\r
1299 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1300 alignPanel.repaint();
\r
1307 * @param e DOCUMENT ME!
\r
1309 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1311 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1312 alignPanel.repaint();
\r
1318 * @param e DOCUMENT ME!
\r
1320 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1322 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1323 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1324 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1325 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1326 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1327 alignPanel.repaint();
\r
1333 * @param e DOCUMENT ME!
\r
1335 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1337 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1338 alignPanel.repaint();
\r
1344 * @param e DOCUMENT ME!
\r
1346 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1348 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1349 alignPanel.repaint();
\r
1355 * @param e DOCUMENT ME!
\r
1357 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1359 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1360 alignPanel.repaint();
\r
1366 * @param e DOCUMENT ME!
\r
1368 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1370 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1371 alignPanel.repaint();
\r
1377 * @param e DOCUMENT ME!
\r
1379 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1381 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1382 alignPanel.repaint();
\r
1388 * @param e DOCUMENT ME!
\r
1390 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1392 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1393 alignPanel.repaint();
\r
1399 * @param evt DOCUMENT ME!
\r
1401 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1403 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1405 if (viewport.showSequenceFeatures &&
\r
1406 ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
\r
1408 System.out.println("new fetcher");
\r
1409 new SequenceFeatureFetcher(viewport.
\r
1414 featureSettings.setEnabled(true);
\r
1416 alignPanel.repaint();
\r
1422 * @param e DOCUMENT ME!
\r
1424 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1426 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1427 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1433 * @param e DOCUMENT ME!
\r
1435 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1437 if (alignPanel.overviewPanel != null)
\r
1442 JInternalFrame frame = new JInternalFrame();
\r
1443 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1444 frame.setContentPane(overview);
\r
1445 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1446 frame.getWidth(), frame.getHeight());
\r
1448 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1449 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1451 public void internalFrameClosed(
\r
1452 javax.swing.event.InternalFrameEvent evt)
\r
1454 alignPanel.setOverviewPanel(null);
\r
1459 alignPanel.setOverviewPanel(overview);
\r
1465 * @param e DOCUMENT ME!
\r
1467 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1469 changeColour(null);
\r
1475 * @param e DOCUMENT ME!
\r
1477 public void clustalColour_actionPerformed(ActionEvent e)
\r
1479 changeColour(new ClustalxColourScheme(
\r
1480 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1486 * @param e DOCUMENT ME!
\r
1488 public void zappoColour_actionPerformed(ActionEvent e)
\r
1490 changeColour(new ZappoColourScheme());
\r
1496 * @param e DOCUMENT ME!
\r
1498 public void taylorColour_actionPerformed(ActionEvent e)
\r
1500 changeColour(new TaylorColourScheme());
\r
1506 * @param e DOCUMENT ME!
\r
1508 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1510 changeColour(new HydrophobicColourScheme());
\r
1516 * @param e DOCUMENT ME!
\r
1518 public void helixColour_actionPerformed(ActionEvent e)
\r
1520 changeColour(new HelixColourScheme());
\r
1526 * @param e DOCUMENT ME!
\r
1528 public void strandColour_actionPerformed(ActionEvent e)
\r
1530 changeColour(new StrandColourScheme());
\r
1536 * @param e DOCUMENT ME!
\r
1538 public void turnColour_actionPerformed(ActionEvent e)
\r
1540 changeColour(new TurnColourScheme());
\r
1546 * @param e DOCUMENT ME!
\r
1548 public void buriedColour_actionPerformed(ActionEvent e)
\r
1550 changeColour(new BuriedColourScheme());
\r
1556 * @param e DOCUMENT ME!
\r
1558 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1560 changeColour(new NucleotideColourScheme());
\r
1566 * @param e DOCUMENT ME!
\r
1568 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1570 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1576 * @param cs DOCUMENT ME!
\r
1578 void changeColour(ColourSchemeI cs)
\r
1580 int threshold = 0;
\r
1584 if (viewport.getAbovePIDThreshold())
\r
1586 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1589 cs.setThreshold(threshold,
\r
1590 viewport.getIgnoreGapsConsensus());
\r
1592 viewport.setGlobalColourScheme(cs);
\r
1596 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1599 if (viewport.getConservationSelected())
\r
1602 Alignment al = (Alignment) viewport.alignment;
\r
1603 Conservation c = new Conservation("All",
\r
1604 ResidueProperties.propHash, 3,
\r
1605 al.getSequences(), 0,
\r
1606 al.getWidth() - 1);
\r
1609 c.verdict(false, viewport.ConsPercGaps);
\r
1611 cs.setConservation(c);
\r
1613 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1618 cs.setConservation(null);
\r
1621 cs.setConsensus(viewport.vconsensus);
\r
1624 viewport.setGlobalColourScheme(cs);
\r
1626 if (viewport.getColourAppliesToAllGroups())
\r
1628 Vector groups = viewport.alignment.getGroups();
\r
1630 for (int i = 0; i < groups.size(); i++)
\r
1632 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1640 if (cs instanceof ClustalxColourScheme)
\r
1642 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1644 else if (cs instanceof UserColourScheme)
\r
1646 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1652 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1654 catch (Exception ex)
\r
1659 if (viewport.getAbovePIDThreshold()
\r
1660 || cs instanceof PIDColourScheme
\r
1661 || cs instanceof Blosum62ColourScheme)
\r
1663 sg.cs.setThreshold(threshold,
\r
1664 viewport.getIgnoreGapsConsensus());
\r
1666 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1670 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1673 if (viewport.getConservationSelected())
\r
1675 Conservation c = new Conservation("Group",
\r
1676 ResidueProperties.propHash, 3,
\r
1678 viewport.alignment.getWidth() - 1);
\r
1680 c.verdict(false, viewport.ConsPercGaps);
\r
1681 sg.cs.setConservation(c);
\r
1684 sg.cs.setConservation(null);
\r
1688 if (alignPanel.getOverviewPanel() != null)
\r
1690 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1693 alignPanel.repaint();
\r
1699 * @param e DOCUMENT ME!
\r
1701 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1703 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1705 SliderPanel.setPIDSliderSource(alignPanel,
\r
1706 viewport.getGlobalColourScheme(),
\r
1708 SliderPanel.showPIDSlider();
\r
1715 * @param e DOCUMENT ME!
\r
1717 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1719 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1721 SliderPanel.setConservationSlider(alignPanel,
\r
1722 viewport.globalColourScheme,
\r
1724 SliderPanel.showConservationSlider();
\r
1731 * @param e DOCUMENT ME!
\r
1733 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1735 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1737 viewport.setAbovePIDThreshold(false);
\r
1738 abovePIDThreshold.setSelected(false);
\r
1740 changeColour(viewport.getGlobalColourScheme());
\r
1742 modifyConservation_actionPerformed(null);
\r
1748 * @param e DOCUMENT ME!
\r
1750 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1752 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1754 conservationMenuItem.setSelected(false);
\r
1755 viewport.setConservationSelected(false);
\r
1757 changeColour(viewport.getGlobalColourScheme());
\r
1759 modifyPID_actionPerformed(null);
\r
1765 * @param e DOCUMENT ME!
\r
1767 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1769 if (e.getActionCommand().equals("User Defined..."))
\r
1771 new UserDefinedColours(alignPanel, null);
\r
1775 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1776 getUserColourSchemes().get(e.getActionCommand());
\r
1778 changeColour(udc);
\r
1782 public void updateUserColourMenu()
\r
1785 Component[] menuItems = colourMenu.getMenuComponents();
\r
1786 int i, iSize = menuItems.length;
\r
1787 for (i = 0; i < iSize; i++)
\r
1789 if (menuItems[i].getName() != null &&
\r
1790 menuItems[i].getName().equals("USER_DEFINED"))
\r
1792 colourMenu.remove(menuItems[i]);
\r
1796 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1798 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1799 getUserColourSchemes().keys();
\r
1801 while (userColours.hasMoreElements())
\r
1803 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1804 nextElement().toString());
\r
1805 radioItem.setName("USER_DEFINED");
\r
1806 radioItem.addMouseListener(new MouseAdapter()
\r
1808 public void mousePressed(MouseEvent evt)
\r
1810 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1812 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1814 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1815 "Remove from default list?",
\r
1816 "Remove user defined colour",
\r
1817 JOptionPane.YES_NO_OPTION);
\r
1818 if(option == JOptionPane.YES_OPTION)
\r
1820 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1821 colourMenu.remove(radioItem);
\r
1824 radioItem.addActionListener(new ActionListener()
\r
1826 public void actionPerformed(ActionEvent evt)
\r
1828 userDefinedColour_actionPerformed(evt);
\r
1834 radioItem.addActionListener(new ActionListener()
\r
1836 public void actionPerformed(ActionEvent evt)
\r
1838 userDefinedColour_actionPerformed(evt);
\r
1842 colourMenu.insert(radioItem, 15);
\r
1843 colours.add(radioItem);
\r
1851 * @param e DOCUMENT ME!
\r
1853 public void PIDColour_actionPerformed(ActionEvent e)
\r
1855 changeColour(new PIDColourScheme());
\r
1861 * @param e DOCUMENT ME!
\r
1863 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1865 changeColour(new Blosum62ColourScheme());
\r
1871 * @param e DOCUMENT ME!
\r
1873 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1875 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1876 HistoryItem.SORT));
\r
1877 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1878 viewport.getAlignment().getSequenceAt(0));
\r
1879 alignPanel.repaint();
\r
1885 * @param e DOCUMENT ME!
\r
1887 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1889 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1890 HistoryItem.SORT));
\r
1891 AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
\r
1892 alignPanel.repaint();
\r
1898 * @param e DOCUMENT ME!
\r
1900 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1902 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1903 HistoryItem.SORT));
\r
1905 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1906 alignPanel.repaint();
\r
1912 * @param e DOCUMENT ME!
\r
1914 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1916 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1917 JInternalFrame frame = new JInternalFrame();
\r
1918 frame.setContentPane(sp);
\r
1919 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1926 * @param e DOCUMENT ME!
\r
1928 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1930 if ( (viewport.getSelectionGroup() == null) ||
\r
1931 (viewport.getSelectionGroup().getSize() < 2))
\r
1933 JOptionPane.showInternalMessageDialog(this,
\r
1934 "You must select at least 2 sequences.",
\r
1935 "Invalid Selection",
\r
1936 JOptionPane.WARNING_MESSAGE);
\r
1940 JInternalFrame frame = new JInternalFrame();
\r
1941 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1942 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1949 * @param e DOCUMENT ME!
\r
1951 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1953 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1954 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1955 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1956 (viewport.getAlignment().getHeight() < 4))
\r
1958 JOptionPane.showInternalMessageDialog(this,
\r
1959 "Principal component analysis must take\n" +
\r
1960 "at least 4 input sequences.",
\r
1961 "Sequence selection insufficient",
\r
1962 JOptionPane.WARNING_MESSAGE);
\r
1967 new PCAPanel(viewport);
\r
1973 * @param e DOCUMENT ME!
\r
1975 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1977 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1983 * @param e DOCUMENT ME!
\r
1985 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1987 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1993 * @param e DOCUMENT ME!
\r
1995 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1997 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2003 * @param e DOCUMENT ME!
\r
2005 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2007 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2013 * @param type DOCUMENT ME!
\r
2014 * @param pwType DOCUMENT ME!
\r
2015 * @param title DOCUMENT ME!
\r
2017 void NewTreePanel(String type, String pwType, String title)
\r
2019 final TreePanel tp;
\r
2021 if ( (viewport.getSelectionGroup() != null) &&
\r
2022 (viewport.getSelectionGroup().getSize() > 3))
\r
2025 SequenceGroup sg = viewport.getSelectionGroup();
\r
2027 /* Decide if the selection is a column region */
\r
2028 while (s < sg.sequences.size())
\r
2030 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2033 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2034 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2035 "Try using the Pad function in the edit menu,\n" +
\r
2036 "or one of the multiple sequence alignment web services.",
\r
2037 "Sequences in selection are not aligned",
\r
2038 JOptionPane.WARNING_MESSAGE);
\r
2044 title = title + " on region";
\r
2045 tp = new TreePanel(viewport,
\r
2046 viewport.getSelectionGroup().sequences, type, pwType,
\r
2047 sg.getStartRes(), sg.getEndRes());
\r
2051 //are the sequences aligned?
\r
2052 if (!viewport.alignment.isAligned())
\r
2054 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2055 "The sequences must be aligned before creating a tree.\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 not aligned",
\r
2059 JOptionPane.WARNING_MESSAGE);
\r
2064 tp = new TreePanel(viewport,
\r
2065 viewport.getAlignment().getSequences(), type, pwType,
\r
2067 viewport.alignment.getWidth());
\r
2070 addTreeMenuItem(tp, title);
\r
2071 viewport.setCurrentTree(tp.getTree());
\r
2073 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2079 * @param title DOCUMENT ME!
\r
2080 * @param order DOCUMENT ME!
\r
2082 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2084 final JMenuItem item = new JMenuItem("by " + title);
\r
2086 item.addActionListener(new java.awt.event.ActionListener()
\r
2088 public void actionPerformed(ActionEvent e)
\r
2090 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2091 HistoryItem.SORT));
\r
2093 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2094 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2095 alignPanel.repaint();
\r
2101 * Maintain the Order by->Displayed Tree menu.
\r
2102 * Creates a new menu item for a TreePanel with an appropriate
\r
2103 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2104 * to remove the menu item when the treePanel is closed, and adjust
\r
2105 * the tree leaf to sequence mapping when the alignment is modified.
\r
2106 * @param treePanel Displayed tree window.
\r
2107 * @param title SortBy menu item title.
\r
2109 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2111 final JMenuItem item = new JMenuItem(title);
\r
2115 if (treeCount == 1)
\r
2117 sort.add(sortByTreeMenu);
\r
2120 sortByTreeMenu.add(item);
\r
2121 item.addActionListener(new java.awt.event.ActionListener()
\r
2123 public void actionPerformed(ActionEvent e)
\r
2125 addHistoryItem(new HistoryItem("Tree Sort",
\r
2126 viewport.alignment, HistoryItem.SORT));
\r
2127 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2128 treePanel.getTree());
\r
2129 alignPanel.repaint();
\r
2133 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2134 InternalFrameAdapter()
\r
2136 public void internalFrameClosed(
\r
2137 javax.swing.event.InternalFrameEvent evt)
\r
2140 sortByTreeMenu.remove(item);
\r
2142 if (treeCount == 0)
\r
2144 sort.remove(sortByTreeMenu);
\r
2152 * Work out whether the whole set of sequences
\r
2153 * or just the selected set will be submitted for multiple alignment.
\r
2156 private SequenceI[] gatherSequencesForAlignment()
\r
2158 // Now, check we have enough sequences
\r
2159 SequenceI[] msa = null;
\r
2161 if ( (viewport.getSelectionGroup() != null) &&
\r
2162 (viewport.getSelectionGroup().getSize() > 1))
\r
2164 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2165 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2167 msa = new SequenceI[sz = seqs.getSize()];
\r
2169 for (int i = 0; i < sz; i++)
\r
2171 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2176 Vector seqs = viewport.getAlignment().getSequences();
\r
2178 if (seqs.size() > 1)
\r
2180 msa = new SequenceI[seqs.size()];
\r
2182 for (int i = 0; i < seqs.size(); i++)
\r
2184 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2192 * Decides what is submitted to a secondary structure prediction service,
\r
2193 * the currently selected sequence, or the currently selected alignment
\r
2194 * (where the first sequence in the set is the one that the prediction
\r
2197 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2199 SequenceI seq = null;
\r
2200 SequenceI[] msa = null;
\r
2202 if ( (viewport.getSelectionGroup() != null) &&
\r
2203 (viewport.getSelectionGroup().getSize() > 0))
\r
2205 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2206 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2208 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2210 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2215 msa = new SequenceI[sz = seqs.getSize()];
\r
2217 for (int i = 0; i < sz; i++)
\r
2219 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2225 Vector seqs = viewport.getAlignment().getSequences();
\r
2227 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2229 seq = (SequenceI) seqs.elementAt(0);
\r
2233 msa = new SequenceI[seqs.size()];
\r
2235 for (int i = 0; i < seqs.size(); i++)
\r
2237 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2249 return new SequenceI[]
\r
2259 * @param e DOCUMENT ME!
\r
2261 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2263 // Pick the tree file
\r
2264 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2266 "LAST_DIRECTORY"));
\r
2267 chooser.setFileView(new JalviewFileView());
\r
2268 chooser.setDialogTitle("Select a newick-like tree file");
\r
2269 chooser.setToolTipText("Load a tree file");
\r
2271 int value = chooser.showOpenDialog(null);
\r
2273 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2275 String choice = chooser.getSelectedFile().getPath();
\r
2276 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2280 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2282 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2284 catch (Exception ex)
\r
2286 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2287 "Problem reading tree file",
\r
2289 JOptionPane.WARNING_MESSAGE);
\r
2290 ex.printStackTrace();
\r
2296 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2298 return ShowNewickTree(nf,title,600,500,4,5);
\r
2303 * @param nf DOCUMENT ME!
\r
2304 * @param title DOCUMENT ME!
\r
2306 * @return DOCUMENT ME!
\r
2308 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2310 TreePanel tp = null;
\r
2316 if (nf.getTree() != null)
\r
2318 tp = new TreePanel(viewport,
\r
2319 viewport.getAlignment().getSequences(), nf,
\r
2326 tp.setLocation(x,y);
\r
2329 Desktop.addInternalFrame(tp, title, w, h);
\r
2330 addTreeMenuItem(tp, title);
\r
2333 catch (Exception ex)
\r
2335 ex.printStackTrace();
\r
2346 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2347 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2348 printJob.setPrintable(alignPanel, pf);
\r
2350 if (printJob.printDialog())
\r
2356 catch (Exception PrintException)
\r
2358 PrintException.printStackTrace();
\r
2365 * Generates menu items and listener event actions for web service clients
\r
2368 public void BuildWebServiceMenu()
\r
2370 if ( (Discoverer.services != null)
\r
2371 && (Discoverer.services.size() > 0))
\r
2373 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2374 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2375 Vector wsmenu = new Vector();
\r
2376 if (msaws != null)
\r
2378 // Add any Multiple Sequence Alignment Services
\r
2379 final JMenu msawsmenu = new JMenu("Alignment");
\r
2380 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2382 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2384 final JMenuItem method = new JMenuItem(sh.getName());
\r
2385 method.addActionListener(new ActionListener()
\r
2387 public void actionPerformed(ActionEvent e)
\r
2389 SequenceI[] msa = gatherSequencesForAlignment();
\r
2390 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2391 false, true, viewport.getAlignment().getDataset());
\r
2396 msawsmenu.add(method);
\r
2397 // Deal with services that we know accept partial alignments.
\r
2398 if (sh.getName().indexOf("lustal") > -1)
\r
2400 // We know that ClustalWS can accept partial alignments for refinement.
\r
2401 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2402 methodR.addActionListener(new ActionListener()
\r
2404 public void actionPerformed(ActionEvent e)
\r
2406 SequenceI[] msa = gatherSequencesForAlignment();
\r
2407 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2408 true, true, viewport.getAlignment().getDataset());
\r
2413 msawsmenu.add(methodR);
\r
2417 wsmenu.add(msawsmenu);
\r
2419 if (secstrpr != null)
\r
2421 // Add any secondary structure prediction services
\r
2422 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2423 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2425 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2427 final JMenuItem method = new JMenuItem(sh.getName());
\r
2428 method.addActionListener(new ActionListener()
\r
2430 public void actionPerformed(ActionEvent e)
\r
2432 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2433 if (msa.length == 1)
\r
2435 // Single Sequence prediction
\r
2436 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2440 if (msa.length > 1)
\r
2442 // Single Sequence prediction
\r
2443 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2449 secstrmenu.add(method);
\r
2451 wsmenu.add(secstrmenu);
\r
2453 this.webService.removeAll();
\r
2454 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2456 webService.add( (JMenu) wsmenu.get(i));
\r
2461 this.webService.removeAll();
\r
2462 this.webService.add(this.webServiceNoServices);
\r
2464 // TODO: add in rediscovery function
\r
2465 // TODO: reduce code redundancy.
\r
2466 // TODO: group services by location as well as function.
\r
2469 public void vamsasStore_actionPerformed(ActionEvent e)
\r
2471 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2472 getProperty("LAST_DIRECTORY"));
\r
2474 chooser.setFileView(new JalviewFileView());
\r
2475 chooser.setDialogTitle("Export to Vamsas file");
\r
2476 chooser.setToolTipText("Export");
\r
2478 int value = chooser.showSaveDialog(this);
\r
2480 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2482 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2483 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
2484 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
2488 public void featureSettings_actionPerformed(ActionEvent e)
\r
2490 new FeatureSettings(viewport, alignPanel);
\r
2495 public void showTranslation_actionPerformed(ActionEvent e)
\r
2498 if(!viewport.alignment.isNucleotide())
\r
2501 viewport.showTranslation(showTranslation.isSelected());
\r
2503 if(!viewport.alignment.isNucleotide())
\r
2506 int s, sSize = viewport.alignment.getHeight();
\r
2507 SequenceI [] newSeq = new SequenceI[sSize];
\r
2510 StringBuffer protein;
\r
2512 for(s=0; s<sSize; s++)
\r
2514 protein = new StringBuffer();
\r
2515 seq = (SequenceI)viewport.alignment.getSequenceAt(s);
\r
2516 resSize = seq.getLength();
\r
2517 for(res = 0; res < resSize; res+=3)
\r
2519 String codon = seq.getSequence(res, res+3);
\r
2520 codon = codon.replace('U', 'T');
\r
2521 String aa = ResidueProperties.codonTranslate(codon);
\r
2523 protein.append(viewport.getGapCharacter());
\r
2524 else if(aa.equals("STOP"))
\r
2525 protein.append("X");
\r
2527 protein.append( aa );
\r
2529 newSeq[s] = new Sequence(seq.getName(), protein.toString());
\r
2533 AlignmentI al = new Alignment(newSeq);
\r
2534 al.setDataset(null);
\r
2537 ////////////////////////////////
\r
2538 // Copy annotations across
\r
2539 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2540 = viewport.alignment.getAlignmentAnnotation();
\r
2542 for (int i = 0; i < annotations.length; i++)
\r
2545 if (annotations[i].label.equals("Quality") ||
\r
2546 annotations[i].label.equals("Conservation") ||
\r
2547 annotations[i].label.equals("Consensus"))
\r
2553 aSize = viewport.alignment.getWidth()/3;
\r
2554 jalview.datamodel.Annotation [] anots =
\r
2555 new jalview.datamodel.Annotation[aSize];
\r
2557 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2559 if( annotations[i].annotations[a]==null
\r
2560 || annotations[i].annotations[a]==null)
\r
2563 anots[a/3] = new Annotation(
\r
2564 annotations[i].annotations[a].displayCharacter,
\r
2565 annotations[i].annotations[a].description,
\r
2566 annotations[i].annotations[a].secondaryStructure,
\r
2567 annotations[i].annotations[a].value,
\r
2568 annotations[i].annotations[a].colour);
\r
2571 jalview.datamodel.AlignmentAnnotation aa
\r
2572 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2573 annotations[i].description, anots );
\r
2574 al.addAnnotation(aa);
\r
2578 // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2579 // NEW_WINDOW_WIDTH,
\r
2580 // NEW_WINDOW_HEIGHT);
\r
2582 AlignViewport newViewport = new AlignViewport(al);
\r
2583 AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2584 tabbedPane.add("Protein", ap);
\r
2585 viewports.add(newViewport);
\r
2586 alignPanels.add(ap);
\r
2589 /////////////////////////
\r
2591 AlignViewport ds = new AlignViewport(al.getDataset());
\r
2592 ds.setDataset(true);
\r
2593 AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2594 tabbedPane.add("Dataset", dap);
\r
2595 viewports.add(ds);
\r
2596 alignPanels.add(dap);
\r
2597 /////////////////////////
\r
2602 public void tabSelected()
\r
2604 int index = tabbedPane.getSelectedIndex();
\r
2605 viewport = (AlignViewport)viewports.elementAt(index);
\r
2606 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r