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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167 Added so Castor Mapping file can obtain Jalview Version
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169 public String getVersion()
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171 return jalview.bin.Cache.getProperty("VERSION");
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178 * @param String DOCUMENT ME!
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181 public void parseGroupsFile(String file)
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185 BufferedReader in = new BufferedReader(new FileReader(file));
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186 SequenceI seq = null;
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187 String line, type, desc, token;
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189 int index, start, end;
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190 StringTokenizer st;
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191 SequenceFeature sf;
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192 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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194 while ( (line = in.readLine()) != null)
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197 st = new StringTokenizer(line, "\t");
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198 if (st.countTokens() == 2)
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200 type = st.nextToken();
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201 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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202 fr.setColour(type, ucs.findColour("A"));
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206 while (st.hasMoreElements())
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208 desc = st.nextToken();
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209 token = st.nextToken();
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210 if (!token.equals("ID_NOT_SPECIFIED"))
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212 index = viewport.alignment.findIndex(viewport.alignment.findName(
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218 index = Integer.parseInt(st.nextToken());
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221 start = Integer.parseInt(st.nextToken());
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222 end = Integer.parseInt(st.nextToken());
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224 seq = viewport.alignment.getSequenceAt(index);
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225 start = seq.findIndex(start) - 1;
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226 end = seq.findIndex(end) - 1;
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228 type = st.nextToken();
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230 if (fr.getColour(type) == null)
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232 // Probably the old style groups file
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233 UserColourScheme ucs = new UserColourScheme(type);
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234 fr.setColour(type, ucs.findColour("A"));
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238 sf = new SequenceFeature(type, desc, "", start, end);
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240 seq.addSequenceFeature(sf);
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243 // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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244 // sg.addSequence(seq, false);
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246 // viewport.alignment.addGroup(sg);
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251 viewport.showSequenceFeatures = true;
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252 ((Alignment)viewport.alignment).featuresAdded = true;
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254 alignPanel.repaint();
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257 catch (Exception ex)
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259 System.out.println("Error parsing groups file: " + ex);
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263 public void fetchSequence_actionPerformed(ActionEvent e)
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265 new SequenceFetcher(this);
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272 * @param e DOCUMENT ME!
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274 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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276 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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281 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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286 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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287 }, currentFileFormat);
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289 chooser.setAcceptAllFileFilterUsed(false);
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290 chooser.setFileView(new JalviewFileView());
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291 chooser.setDialogTitle("Save Alignment to file");
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292 chooser.setToolTipText("Save");
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294 int value = chooser.showSaveDialog(this);
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296 if (value == JalviewFileChooser.APPROVE_OPTION)
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298 currentFileFormat = chooser.getSelectedFormat();
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300 if (currentFileFormat == null)
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302 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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303 "You must select a file format before saving!",
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304 "File format not specified",
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305 JOptionPane.WARNING_MESSAGE);
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306 value = chooser.showSaveDialog(this);
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310 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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311 currentFileFormat);
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313 String choice = chooser.getSelectedFile().getPath();
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314 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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316 saveAlignment(choice, currentFileFormat);
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320 public boolean saveAlignment(String file, String format)
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322 if (format.equalsIgnoreCase("Jalview"))
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324 String shortName = title;
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326 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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328 shortName = shortName.substring(shortName.lastIndexOf(
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329 java.io.File.separatorChar) + 1);
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332 Jalview2XML.SaveAlignment(this, file, shortName);
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334 // USE Jalview2XML to save this file
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339 String output = new FormatAdapter().formatSequences(format,
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340 viewport.getAlignment().
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342 if (output == null)
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349 java.io.PrintWriter out = new java.io.PrintWriter(
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350 new java.io.FileWriter(file));
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356 catch (Exception ex)
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358 ex.printStackTrace();
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367 * @param e DOCUMENT ME!
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369 protected void outputText_actionPerformed(ActionEvent e)
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371 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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372 Desktop.addInternalFrame(cap,
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373 "Alignment output - " + e.getActionCommand(), 600,
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375 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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376 viewport.getAlignment().
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383 * @param e DOCUMENT ME!
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385 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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387 new HTMLOutput(viewport);
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390 public void createImageMap(File file, String image)
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392 alignPanel.makePNGImageMap(file, image);
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398 * @param e DOCUMENT ME!
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400 public void createPNG(File f)
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402 alignPanel.makePNG(f);
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408 * @param e DOCUMENT ME!
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410 public void createEPS(File f)
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412 alignPanel.makeEPS(f);
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418 * @param e DOCUMENT ME!
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420 public void printMenuItem_actionPerformed(ActionEvent e)
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422 //Putting in a thread avoids Swing painting problems
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423 PrintThread thread = new PrintThread();
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430 * @param e DOCUMENT ME!
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432 public void closeMenuItem_actionPerformed(ActionEvent e)
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436 PaintRefresher.components.remove(viewport.alignment);
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437 this.setClosed(true);
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439 catch (Exception ex)
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447 void updateEditMenuBar()
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449 if (historyList.size() > 0)
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451 undoMenuItem.setEnabled(true);
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453 HistoryItem hi = (HistoryItem) historyList.peek();
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454 undoMenuItem.setText("Undo " + hi.getDescription());
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458 undoMenuItem.setEnabled(false);
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459 undoMenuItem.setText("Undo");
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462 if (redoList.size() > 0)
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464 redoMenuItem.setEnabled(true);
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466 HistoryItem hi = (HistoryItem) redoList.peek();
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467 redoMenuItem.setText("Redo " + hi.getDescription());
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471 redoMenuItem.setEnabled(false);
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472 redoMenuItem.setText("Redo");
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479 * @param hi DOCUMENT ME!
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481 public void addHistoryItem(HistoryItem hi)
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483 historyList.push(hi);
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484 updateEditMenuBar();
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490 * @param e DOCUMENT ME!
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492 protected void undoMenuItem_actionPerformed(ActionEvent e)
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494 HistoryItem hi = (HistoryItem) historyList.pop();
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495 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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496 HistoryItem.HIDE));
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497 restoreHistoryItem(hi);
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498 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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504 * @param e DOCUMENT ME!
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506 protected void redoMenuItem_actionPerformed(ActionEvent e)
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508 HistoryItem hi = (HistoryItem) redoList.pop();
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509 restoreHistoryItem(hi);
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510 updateEditMenuBar();
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511 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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514 // used by undo and redo
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515 void restoreHistoryItem(HistoryItem hi)
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517 if (hi.getType() == HistoryItem.SORT)
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519 for (int i = 0; i < hi.getSequences().size(); i++)
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521 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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528 for (int i = 0; i < hi.getSequences().size(); i++)
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530 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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532 if (restore.getLength() == 0)
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534 restore.setSequence(hi.getHidden().elementAt(i).toString());
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535 viewport.alignment.getSequences().insertElementAt(restore,
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536 hi.getAlignIndex(i));
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540 restore.setSequence(hi.getHidden().elementAt(i).toString());
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544 if (hi.getType() == HistoryItem.PASTE)
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546 for (int i = viewport.alignment.getHeight() - 1;
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547 i > (hi.getSequences().size() - 1); i--)
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549 viewport.alignment.deleteSequence(i);
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554 updateEditMenuBar();
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556 viewport.firePropertyChange("alignment", null,
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557 viewport.getAlignment().getSequences());
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563 * @param up DOCUMENT ME!
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565 public void moveSelectedSequences(boolean up)
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567 SequenceGroup sg = viewport.getSelectionGroup();
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576 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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578 SequenceI seq = viewport.alignment.getSequenceAt(i);
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580 if (!sg.sequences.contains(seq))
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585 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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587 if (sg.sequences.contains(temp))
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592 viewport.alignment.getSequences().setElementAt(temp, i);
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593 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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598 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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600 SequenceI seq = viewport.alignment.getSequenceAt(i);
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602 if (!sg.sequences.contains(seq))
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607 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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609 if (sg.sequences.contains(temp))
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614 viewport.alignment.getSequences().setElementAt(temp, i);
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615 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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619 alignPanel.repaint();
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622 public void lostOwnership(Clipboard clipboard, Transferable contents)
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624 Desktop.jalviewClipboard = null;
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631 * @param e DOCUMENT ME!
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633 protected void copy_actionPerformed(ActionEvent e)
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635 if (viewport.getSelectionGroup() == null)
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640 SequenceGroup sg = viewport.getSelectionGroup();
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642 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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644 Hashtable orderedSeqs = new Hashtable();
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645 SequenceI[] seqs = new SequenceI[sg.getSize()];
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647 for (int i = 0; i < sg.getSize(); i++)
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649 SequenceI seq = sg.getSequenceAt(i);
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650 int index = viewport.alignment.findIndex(seq);
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651 orderedSeqs.put(index + "", seq);
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654 int index = 0, startRes, endRes;
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657 for (int i = 0; i < sg.getSize(); i++)
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659 SequenceI seq = null;
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661 while (seq == null)
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663 if (orderedSeqs.containsKey(index + ""))
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665 seq = (SequenceI) orderedSeqs.get(index + "");
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677 //Returns residue following index if gap
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678 startRes = seq.findPosition(sg.getStartRes());
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681 //Need to find the residue preceeding index if gap
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684 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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686 ch = seq.getCharAt(j);
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687 if (!jalview.util.Comparison.isGap( (ch)))
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695 endRes += seq.getStart() - 1;
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698 seqs[i] = new Sequence(seq.getName(),
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699 seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
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702 seqs[i].setDescription(seq.getDescription());
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703 seqs[i].setDBRef(seq.getDBRef());
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704 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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705 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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709 FastaFile ff = new FastaFile();
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710 ff.addDBPrefix( viewport.showDBPrefix );
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711 ff.addJVSuffix( viewport.showJVSuffix );
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712 c.setContents(new StringSelection( ff.print(seqs)), this);
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713 Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};
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719 * @param e DOCUMENT ME!
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721 protected void pasteNew_actionPerformed(ActionEvent e)
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729 * @param e DOCUMENT ME!
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731 protected void pasteThis_actionPerformed(ActionEvent e)
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733 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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734 HistoryItem.PASTE));
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741 * @param newAlignment DOCUMENT ME!
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743 void paste(boolean newAlignment)
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747 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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748 Transferable contents = c.getContents(this);
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750 if (contents == null)
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755 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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759 String format = IdentifyFile.Identify(str, "Paste");
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760 SequenceI[] sequences;
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762 if(Desktop.jalviewClipboard!=null)
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764 // The clipboard was filled from within Jalview, we must use the sequences
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765 // And dataset from the copied alignment
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766 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
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770 sequences = new FormatAdapter().readFile(str, "Paste", format);
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776 Alignment alignment = new Alignment(sequences);
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778 if(Desktop.jalviewClipboard!=null)
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779 alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
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781 alignment.setDataset( null );
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784 AlignFrame af = new AlignFrame(alignment);
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785 String newtitle = new String("Copied sequences");
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787 if (title.startsWith("Copied sequences"))
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793 newtitle = newtitle.concat("- from " + title);
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796 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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797 NEW_WINDOW_HEIGHT);
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802 for (int i = 0; i < sequences.length; i++)
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804 viewport.alignment.addSequence(sequences[i]);
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805 if(sequences[i].getDatasetSequence()==null)
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807 ////////////////////////////
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808 //Datset needs extension;
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809 /////////////////////////////
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810 Sequence ds = new Sequence(sequences[i].getName(),
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811 AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
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812 sequences[i].getStart(),
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813 sequences[i].getEnd());
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814 sequences[i].setDatasetSequence(ds);
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815 viewport.alignment.getDataset().addSequence(ds);
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821 viewport.setEndSeq(viewport.alignment.getHeight());
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822 viewport.alignment.getWidth();
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823 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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826 catch (Exception ex)
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828 // could be anything being pasted in here
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837 * @param e DOCUMENT ME!
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839 protected void cut_actionPerformed(ActionEvent e)
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841 copy_actionPerformed(null);
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842 delete_actionPerformed(null);
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848 * @param e DOCUMENT ME!
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850 protected void delete_actionPerformed(ActionEvent e)
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853 if (viewport.getSelectionGroup() == null)
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858 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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859 HistoryItem.HIDE));
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861 SequenceGroup sg = viewport.getSelectionGroup();
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862 boolean allSequences = false;
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863 if (sg.sequences.size() == viewport.alignment.getHeight())
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865 allSequences = true;
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868 for (int i = 0; i < sg.sequences.size(); i++)
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870 SequenceI seq = sg.getSequenceAt(i);
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871 int index = viewport.getAlignment().findIndex(seq);
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872 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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874 // If the cut affects all sequences, remove highlighted columns
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877 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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878 sg.getEndRes() + 1);
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881 if (seq.getSequence().length() < 1)
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883 viewport.getAlignment().deleteSequence(seq);
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887 viewport.getAlignment().getSequences().setElementAt(seq, index);
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891 viewport.setSelectionGroup(null);
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892 viewport.alignment.deleteGroup(sg);
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894 viewport.firePropertyChange("alignment", null,
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895 viewport.getAlignment().getSequences());
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899 if (viewport.getAlignment().getHeight() < 1)
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903 this.setClosed(true);
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905 catch (Exception ex)
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914 * @param e DOCUMENT ME!
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916 protected void deleteGroups_actionPerformed(ActionEvent e)
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918 viewport.alignment.deleteAllGroups();
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919 viewport.setSelectionGroup(null);
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920 alignPanel.repaint();
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926 * @param e DOCUMENT ME!
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928 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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930 SequenceGroup sg = new SequenceGroup();
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932 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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935 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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938 sg.setEndRes(viewport.alignment.getWidth() - 1);
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939 viewport.setSelectionGroup(sg);
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940 PaintRefresher.Refresh(null, viewport.alignment);
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946 * @param e DOCUMENT ME!
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948 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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950 viewport.setSelectionGroup(null);
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951 viewport.getColumnSelection().clear();
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952 viewport.setSelectionGroup(null);
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953 alignPanel.annotationPanel.activeRes = null;
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954 PaintRefresher.Refresh(null, viewport.alignment);
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960 * @param e DOCUMENT ME!
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962 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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964 SequenceGroup sg = viewport.getSelectionGroup();
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968 selectAllSequenceMenuItem_actionPerformed(null);
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973 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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976 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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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 remove2LeftMenuItem_actionPerformed(ActionEvent e)
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989 ColumnSelection colSel = viewport.getColumnSelection();
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991 if (colSel.size() > 0)
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993 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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994 HistoryItem.HIDE));
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996 int min = colSel.getMin();
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997 viewport.getAlignment().trimLeft(min);
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998 colSel.compensateForEdit(0, min);
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1000 if (viewport.getSelectionGroup() != null)
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1002 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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1005 Vector groups = viewport.alignment.getGroups();
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1007 for (int i = 0; i < groups.size(); i++)
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1009 SequenceGroup sg = (SequenceGroup) groups.get(i);
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1011 if (!sg.adjustForRemoveLeft(min))
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1013 viewport.alignment.deleteGroup(sg);
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1017 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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1024 * @param e DOCUMENT ME!
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1026 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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1028 ColumnSelection colSel = viewport.getColumnSelection();
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1030 if (colSel.size() > 0)
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1032 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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1033 HistoryItem.HIDE));
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1035 int max = colSel.getMax();
\r
1036 viewport.getAlignment().trimRight(max);
\r
1038 if (viewport.getSelectionGroup() != null)
\r
1040 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1043 Vector groups = viewport.alignment.getGroups();
\r
1045 for (int i = 0; i < groups.size(); i++)
\r
1047 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1049 if (!sg.adjustForRemoveRight(max))
\r
1051 viewport.alignment.deleteGroup(sg);
\r
1055 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1062 * @param e DOCUMENT ME!
\r
1064 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1066 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1067 viewport.alignment, HistoryItem.HIDE));
\r
1069 //This is to maintain viewport position on first residue
\r
1070 //of first sequence
\r
1071 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1072 int startRes = seq.findPosition(viewport.startRes);
\r
1074 viewport.getAlignment().removeGaps();
\r
1076 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1078 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1084 * @param e DOCUMENT ME!
\r
1086 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1088 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1089 HistoryItem.HIDE));
\r
1091 //This is to maintain viewport position on first residue
\r
1092 //of first sequence
\r
1093 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1094 int startRes = seq.findPosition(viewport.startRes);
\r
1097 SequenceI current;
\r
1100 Vector seqs = null;
\r
1103 int end = viewport.alignment.getWidth();
\r
1105 if (viewport.getSelectionGroup() != null
\r
1106 && viewport.getSelectionGroup().sequences != null
\r
1107 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1109 seqs = viewport.getSelectionGroup().sequences;
\r
1110 start = viewport.getSelectionGroup().getStartRes();
\r
1111 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1115 seqs = viewport.alignment.getSequences();
\r
1118 for (int i = 0; i < seqs.size(); i++)
\r
1120 current = (SequenceI) seqs.elementAt(i);
\r
1121 jSize = current.getLength();
\r
1123 // Removing a range is much quicker than removing gaps
\r
1124 // one by one for long sequences
\r
1126 int rangeStart=-1, rangeEnd=-1;
\r
1130 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1132 if(rangeStart==-1)
\r
1147 current.deleteChars(rangeStart, rangeEnd);
\r
1148 j-=rangeEnd-rangeStart;
\r
1149 jSize-=rangeEnd-rangeStart;
\r
1157 while (j < end && j < jSize);
\r
1160 current.deleteChars(rangeStart, rangeEnd);
\r
1164 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1166 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1169 public void alignmentChanged()
\r
1171 if(viewport.vconsensus!=null)
\r
1173 viewport.updateConsensus();
\r
1174 viewport.updateConservation();
\r
1176 resetAllColourSchemes();
\r
1177 if(alignPanel.overviewPanel!=null)
\r
1178 alignPanel.overviewPanel.updateOverviewImage();
\r
1180 Provenance prov = viewport.alignment.getProvenance();
\r
1183 prov = new Provenance();
\r
1184 viewport.alignment.setProvenance(prov);
\r
1187 prov.addEntry("Me",
\r
1188 "Edited in Jalview", new java.util.Date(), "myID");
\r
1190 alignPanel.repaint();
\r
1193 void resetAllColourSchemes()
\r
1195 ColourSchemeI cs = viewport.globalColourScheme;
\r
1198 if (cs instanceof ClustalxColourScheme)
\r
1200 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1201 resetClustalX(viewport.alignment.getSequences(),
\r
1202 viewport.alignment.getWidth());
\r
1205 cs.setConsensus(viewport.vconsensus);
\r
1206 if (cs.conservationApplied())
\r
1208 Alignment al = (Alignment) viewport.alignment;
\r
1209 Conservation c = new Conservation("All",
\r
1210 ResidueProperties.propHash, 3,
\r
1211 al.getSequences(), 0,
\r
1212 al.getWidth() - 1);
\r
1214 c.verdict(false, viewport.ConsPercGaps);
\r
1216 cs.setConservation(c);
\r
1220 int s, sSize = viewport.alignment.getGroups().size();
\r
1221 for(s=0; s<sSize; s++)
\r
1223 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1224 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1226 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1228 sg.recalcConservation();
\r
1235 * @param e DOCUMENT ME!
\r
1237 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1239 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1240 HistoryItem.HIDE));
\r
1242 SequenceI current;
\r
1243 int Width = viewport.getAlignment().getWidth();
\r
1245 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1248 current = viewport.getAlignment().getSequenceAt(i);
\r
1250 if (current.getLength() < Width)
\r
1252 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1256 alignmentChanged();
\r
1262 * @param e DOCUMENT ME!
\r
1264 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1266 JInternalFrame frame = new JInternalFrame();
\r
1267 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1268 frame.setContentPane(finder);
\r
1269 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1270 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1276 * @param e DOCUMENT ME!
\r
1278 public void font_actionPerformed(ActionEvent e)
\r
1280 new FontChooser(alignPanel);
\r
1286 * @param e DOCUMENT ME!
\r
1288 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1290 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1292 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1293 alignPanel.repaint();
\r
1296 public void seqDBRef_actionPerformed(ActionEvent e)
\r
1298 viewport.setShowDBPrefix(seqDBRef.isSelected());
\r
1300 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1301 alignPanel.repaint();
\r
1308 * @param e DOCUMENT ME!
\r
1310 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1312 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1313 alignPanel.repaint();
\r
1319 * @param e DOCUMENT ME!
\r
1321 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1323 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1324 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1325 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1326 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1327 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1328 alignPanel.repaint();
\r
1334 * @param e DOCUMENT ME!
\r
1336 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1338 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1339 alignPanel.repaint();
\r
1345 * @param e DOCUMENT ME!
\r
1347 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1349 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1350 alignPanel.repaint();
\r
1356 * @param e DOCUMENT ME!
\r
1358 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1360 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1361 alignPanel.repaint();
\r
1367 * @param e DOCUMENT ME!
\r
1369 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1371 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1372 alignPanel.repaint();
\r
1378 * @param e DOCUMENT ME!
\r
1380 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1382 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1383 alignPanel.repaint();
\r
1389 * @param e DOCUMENT ME!
\r
1391 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1393 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1394 alignPanel.repaint();
\r
1400 * @param evt DOCUMENT ME!
\r
1402 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1404 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1406 if (viewport.showSequenceFeatures &&
\r
1407 ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
\r
1409 System.out.println("new fetcher");
\r
1410 new SequenceFeatureFetcher(viewport.
\r
1415 featureSettings.setEnabled(true);
\r
1417 alignPanel.repaint();
\r
1423 * @param e DOCUMENT ME!
\r
1425 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1427 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1428 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1434 * @param e DOCUMENT ME!
\r
1436 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1438 if (alignPanel.overviewPanel != null)
\r
1443 JInternalFrame frame = new JInternalFrame();
\r
1444 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1445 frame.setContentPane(overview);
\r
1446 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1447 frame.getWidth(), frame.getHeight());
\r
1449 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1450 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1452 public void internalFrameClosed(
\r
1453 javax.swing.event.InternalFrameEvent evt)
\r
1455 alignPanel.setOverviewPanel(null);
\r
1460 alignPanel.setOverviewPanel(overview);
\r
1466 * @param e DOCUMENT ME!
\r
1468 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1470 changeColour(null);
\r
1476 * @param e DOCUMENT ME!
\r
1478 public void clustalColour_actionPerformed(ActionEvent e)
\r
1480 changeColour(new ClustalxColourScheme(
\r
1481 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1487 * @param e DOCUMENT ME!
\r
1489 public void zappoColour_actionPerformed(ActionEvent e)
\r
1491 changeColour(new ZappoColourScheme());
\r
1497 * @param e DOCUMENT ME!
\r
1499 public void taylorColour_actionPerformed(ActionEvent e)
\r
1501 changeColour(new TaylorColourScheme());
\r
1507 * @param e DOCUMENT ME!
\r
1509 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1511 changeColour(new HydrophobicColourScheme());
\r
1517 * @param e DOCUMENT ME!
\r
1519 public void helixColour_actionPerformed(ActionEvent e)
\r
1521 changeColour(new HelixColourScheme());
\r
1527 * @param e DOCUMENT ME!
\r
1529 public void strandColour_actionPerformed(ActionEvent e)
\r
1531 changeColour(new StrandColourScheme());
\r
1537 * @param e DOCUMENT ME!
\r
1539 public void turnColour_actionPerformed(ActionEvent e)
\r
1541 changeColour(new TurnColourScheme());
\r
1547 * @param e DOCUMENT ME!
\r
1549 public void buriedColour_actionPerformed(ActionEvent e)
\r
1551 changeColour(new BuriedColourScheme());
\r
1557 * @param e DOCUMENT ME!
\r
1559 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1561 changeColour(new NucleotideColourScheme());
\r
1567 * @param e DOCUMENT ME!
\r
1569 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1571 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1577 * @param cs DOCUMENT ME!
\r
1579 void changeColour(ColourSchemeI cs)
\r
1581 int threshold = 0;
\r
1585 if (viewport.getAbovePIDThreshold())
\r
1587 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1590 cs.setThreshold(threshold,
\r
1591 viewport.getIgnoreGapsConsensus());
\r
1593 viewport.setGlobalColourScheme(cs);
\r
1597 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1600 if (viewport.getConservationSelected())
\r
1603 Alignment al = (Alignment) viewport.alignment;
\r
1604 Conservation c = new Conservation("All",
\r
1605 ResidueProperties.propHash, 3,
\r
1606 al.getSequences(), 0,
\r
1607 al.getWidth() - 1);
\r
1610 c.verdict(false, viewport.ConsPercGaps);
\r
1612 cs.setConservation(c);
\r
1614 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1619 cs.setConservation(null);
\r
1622 cs.setConsensus(viewport.vconsensus);
\r
1625 viewport.setGlobalColourScheme(cs);
\r
1627 if (viewport.getColourAppliesToAllGroups())
\r
1629 Vector groups = viewport.alignment.getGroups();
\r
1631 for (int i = 0; i < groups.size(); i++)
\r
1633 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1641 if (cs instanceof ClustalxColourScheme)
\r
1643 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1645 else if (cs instanceof UserColourScheme)
\r
1647 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1653 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1655 catch (Exception ex)
\r
1660 if (viewport.getAbovePIDThreshold()
\r
1661 || cs instanceof PIDColourScheme
\r
1662 || cs instanceof Blosum62ColourScheme)
\r
1664 sg.cs.setThreshold(threshold,
\r
1665 viewport.getIgnoreGapsConsensus());
\r
1667 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1671 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1674 if (viewport.getConservationSelected())
\r
1676 Conservation c = new Conservation("Group",
\r
1677 ResidueProperties.propHash, 3,
\r
1679 viewport.alignment.getWidth() - 1);
\r
1681 c.verdict(false, viewport.ConsPercGaps);
\r
1682 sg.cs.setConservation(c);
\r
1685 sg.cs.setConservation(null);
\r
1689 if (alignPanel.getOverviewPanel() != null)
\r
1691 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1694 alignPanel.repaint();
\r
1700 * @param e DOCUMENT ME!
\r
1702 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1704 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1706 SliderPanel.setPIDSliderSource(alignPanel,
\r
1707 viewport.getGlobalColourScheme(),
\r
1709 SliderPanel.showPIDSlider();
\r
1716 * @param e DOCUMENT ME!
\r
1718 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1720 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1722 SliderPanel.setConservationSlider(alignPanel,
\r
1723 viewport.globalColourScheme,
\r
1725 SliderPanel.showConservationSlider();
\r
1732 * @param e DOCUMENT ME!
\r
1734 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1736 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1738 viewport.setAbovePIDThreshold(false);
\r
1739 abovePIDThreshold.setSelected(false);
\r
1741 changeColour(viewport.getGlobalColourScheme());
\r
1743 modifyConservation_actionPerformed(null);
\r
1749 * @param e DOCUMENT ME!
\r
1751 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1753 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1755 conservationMenuItem.setSelected(false);
\r
1756 viewport.setConservationSelected(false);
\r
1758 changeColour(viewport.getGlobalColourScheme());
\r
1760 modifyPID_actionPerformed(null);
\r
1766 * @param e DOCUMENT ME!
\r
1768 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1770 if (e.getActionCommand().equals("User Defined..."))
\r
1772 new UserDefinedColours(alignPanel, null);
\r
1776 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1777 getUserColourSchemes().get(e.getActionCommand());
\r
1779 changeColour(udc);
\r
1783 public void updateUserColourMenu()
\r
1786 Component[] menuItems = colourMenu.getMenuComponents();
\r
1787 int i, iSize = menuItems.length;
\r
1788 for (i = 0; i < iSize; i++)
\r
1790 if (menuItems[i].getName() != null &&
\r
1791 menuItems[i].getName().equals("USER_DEFINED"))
\r
1793 colourMenu.remove(menuItems[i]);
\r
1797 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1799 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1800 getUserColourSchemes().keys();
\r
1802 while (userColours.hasMoreElements())
\r
1804 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1805 nextElement().toString());
\r
1806 radioItem.setName("USER_DEFINED");
\r
1807 radioItem.addMouseListener(new MouseAdapter()
\r
1809 public void mousePressed(MouseEvent evt)
\r
1811 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1813 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1815 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1816 "Remove from default list?",
\r
1817 "Remove user defined colour",
\r
1818 JOptionPane.YES_NO_OPTION);
\r
1819 if(option == JOptionPane.YES_OPTION)
\r
1821 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1822 colourMenu.remove(radioItem);
\r
1825 radioItem.addActionListener(new ActionListener()
\r
1827 public void actionPerformed(ActionEvent evt)
\r
1829 userDefinedColour_actionPerformed(evt);
\r
1835 radioItem.addActionListener(new ActionListener()
\r
1837 public void actionPerformed(ActionEvent evt)
\r
1839 userDefinedColour_actionPerformed(evt);
\r
1843 colourMenu.insert(radioItem, 15);
\r
1844 colours.add(radioItem);
\r
1852 * @param e DOCUMENT ME!
\r
1854 public void PIDColour_actionPerformed(ActionEvent e)
\r
1856 changeColour(new PIDColourScheme());
\r
1862 * @param e DOCUMENT ME!
\r
1864 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1866 changeColour(new Blosum62ColourScheme());
\r
1872 * @param e DOCUMENT ME!
\r
1874 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1876 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1877 HistoryItem.SORT));
\r
1878 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1879 viewport.getAlignment().getSequenceAt(0));
\r
1880 alignPanel.repaint();
\r
1886 * @param e DOCUMENT ME!
\r
1888 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1890 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1891 HistoryItem.SORT));
\r
1892 AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
\r
1893 alignPanel.repaint();
\r
1899 * @param e DOCUMENT ME!
\r
1901 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1903 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1904 HistoryItem.SORT));
\r
1906 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1907 alignPanel.repaint();
\r
1913 * @param e DOCUMENT ME!
\r
1915 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1917 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1918 JInternalFrame frame = new JInternalFrame();
\r
1919 frame.setContentPane(sp);
\r
1920 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1927 * @param e DOCUMENT ME!
\r
1929 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1931 if ( (viewport.getSelectionGroup() == null) ||
\r
1932 (viewport.getSelectionGroup().getSize() < 2))
\r
1934 JOptionPane.showInternalMessageDialog(this,
\r
1935 "You must select at least 2 sequences.",
\r
1936 "Invalid Selection",
\r
1937 JOptionPane.WARNING_MESSAGE);
\r
1941 JInternalFrame frame = new JInternalFrame();
\r
1942 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1943 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1950 * @param e DOCUMENT ME!
\r
1952 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1954 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1955 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1956 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1957 (viewport.getAlignment().getHeight() < 4))
\r
1959 JOptionPane.showInternalMessageDialog(this,
\r
1960 "Principal component analysis must take\n" +
\r
1961 "at least 4 input sequences.",
\r
1962 "Sequence selection insufficient",
\r
1963 JOptionPane.WARNING_MESSAGE);
\r
1968 new PCAPanel(viewport);
\r
1974 * @param e DOCUMENT ME!
\r
1976 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1978 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1984 * @param e DOCUMENT ME!
\r
1986 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1988 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1994 * @param e DOCUMENT ME!
\r
1996 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1998 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2004 * @param e DOCUMENT ME!
\r
2006 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2008 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2014 * @param type DOCUMENT ME!
\r
2015 * @param pwType DOCUMENT ME!
\r
2016 * @param title DOCUMENT ME!
\r
2018 void NewTreePanel(String type, String pwType, String title)
\r
2020 final TreePanel tp;
\r
2022 if ( (viewport.getSelectionGroup() != null) &&
\r
2023 (viewport.getSelectionGroup().getSize() > 3))
\r
2026 SequenceGroup sg = viewport.getSelectionGroup();
\r
2028 /* Decide if the selection is a column region */
\r
2029 while (s < sg.sequences.size())
\r
2031 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2034 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2035 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2036 "Try using the Pad function in the edit menu,\n" +
\r
2037 "or one of the multiple sequence alignment web services.",
\r
2038 "Sequences in selection are not aligned",
\r
2039 JOptionPane.WARNING_MESSAGE);
\r
2045 title = title + " on region";
\r
2046 tp = new TreePanel(viewport,
\r
2047 viewport.getSelectionGroup().sequences, type, pwType,
\r
2048 sg.getStartRes(), sg.getEndRes());
\r
2052 //are the sequences aligned?
\r
2053 if (!viewport.alignment.isAligned())
\r
2055 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2056 "The sequences must be aligned before creating a tree.\n" +
\r
2057 "Try using the Pad function in the edit menu,\n" +
\r
2058 "or one of the multiple sequence alignment web services.",
\r
2059 "Sequences not aligned",
\r
2060 JOptionPane.WARNING_MESSAGE);
\r
2065 tp = new TreePanel(viewport,
\r
2066 viewport.getAlignment().getSequences(), type, pwType,
\r
2068 viewport.alignment.getWidth());
\r
2071 addTreeMenuItem(tp, title);
\r
2072 viewport.setCurrentTree(tp.getTree());
\r
2074 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2080 * @param title DOCUMENT ME!
\r
2081 * @param order DOCUMENT ME!
\r
2083 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2085 final JMenuItem item = new JMenuItem("by " + title);
\r
2087 item.addActionListener(new java.awt.event.ActionListener()
\r
2089 public void actionPerformed(ActionEvent e)
\r
2091 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2092 HistoryItem.SORT));
\r
2094 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2095 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2096 alignPanel.repaint();
\r
2102 * Maintain the Order by->Displayed Tree menu.
\r
2103 * Creates a new menu item for a TreePanel with an appropriate
\r
2104 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2105 * to remove the menu item when the treePanel is closed, and adjust
\r
2106 * the tree leaf to sequence mapping when the alignment is modified.
\r
2107 * @param treePanel Displayed tree window.
\r
2108 * @param title SortBy menu item title.
\r
2110 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2112 final JMenuItem item = new JMenuItem(title);
\r
2116 if (treeCount == 1)
\r
2118 sort.add(sortByTreeMenu);
\r
2121 sortByTreeMenu.add(item);
\r
2122 item.addActionListener(new java.awt.event.ActionListener()
\r
2124 public void actionPerformed(ActionEvent e)
\r
2126 addHistoryItem(new HistoryItem("Tree Sort",
\r
2127 viewport.alignment, HistoryItem.SORT));
\r
2128 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2129 treePanel.getTree());
\r
2130 alignPanel.repaint();
\r
2134 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2135 InternalFrameAdapter()
\r
2137 public void internalFrameClosed(
\r
2138 javax.swing.event.InternalFrameEvent evt)
\r
2141 sortByTreeMenu.remove(item);
\r
2143 if (treeCount == 0)
\r
2145 sort.remove(sortByTreeMenu);
\r
2153 * Work out whether the whole set of sequences
\r
2154 * or just the selected set will be submitted for multiple alignment.
\r
2157 private SequenceI[] gatherSequencesForAlignment()
\r
2159 // Now, check we have enough sequences
\r
2160 SequenceI[] msa = null;
\r
2162 if ( (viewport.getSelectionGroup() != null) &&
\r
2163 (viewport.getSelectionGroup().getSize() > 1))
\r
2165 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2166 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2168 msa = new SequenceI[sz = seqs.getSize()];
\r
2170 for (int i = 0; i < sz; i++)
\r
2172 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2177 Vector seqs = viewport.getAlignment().getSequences();
\r
2179 if (seqs.size() > 1)
\r
2181 msa = new SequenceI[seqs.size()];
\r
2183 for (int i = 0; i < seqs.size(); i++)
\r
2185 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2193 * Decides what is submitted to a secondary structure prediction service,
\r
2194 * the currently selected sequence, or the currently selected alignment
\r
2195 * (where the first sequence in the set is the one that the prediction
\r
2198 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2200 SequenceI seq = null;
\r
2201 SequenceI[] msa = null;
\r
2203 if ( (viewport.getSelectionGroup() != null) &&
\r
2204 (viewport.getSelectionGroup().getSize() > 0))
\r
2206 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2207 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2209 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2211 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2216 msa = new SequenceI[sz = seqs.getSize()];
\r
2218 for (int i = 0; i < sz; i++)
\r
2220 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2226 Vector seqs = viewport.getAlignment().getSequences();
\r
2228 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2230 seq = (SequenceI) seqs.elementAt(0);
\r
2234 msa = new SequenceI[seqs.size()];
\r
2236 for (int i = 0; i < seqs.size(); i++)
\r
2238 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2250 return new SequenceI[]
\r
2260 * @param e DOCUMENT ME!
\r
2262 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2264 // Pick the tree file
\r
2265 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2267 "LAST_DIRECTORY"));
\r
2268 chooser.setFileView(new JalviewFileView());
\r
2269 chooser.setDialogTitle("Select a newick-like tree file");
\r
2270 chooser.setToolTipText("Load a tree file");
\r
2272 int value = chooser.showOpenDialog(null);
\r
2274 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2276 String choice = chooser.getSelectedFile().getPath();
\r
2277 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2281 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2283 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2285 catch (Exception ex)
\r
2287 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2288 "Problem reading tree file",
\r
2290 JOptionPane.WARNING_MESSAGE);
\r
2291 ex.printStackTrace();
\r
2297 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2299 return ShowNewickTree(nf,title,600,500,4,5);
\r
2304 * @param nf DOCUMENT ME!
\r
2305 * @param title DOCUMENT ME!
\r
2307 * @return DOCUMENT ME!
\r
2309 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2311 TreePanel tp = null;
\r
2317 if (nf.getTree() != null)
\r
2319 tp = new TreePanel(viewport,
\r
2320 viewport.getAlignment().getSequences(), nf,
\r
2327 tp.setLocation(x,y);
\r
2330 Desktop.addInternalFrame(tp, title, w, h);
\r
2331 addTreeMenuItem(tp, title);
\r
2334 catch (Exception ex)
\r
2336 ex.printStackTrace();
\r
2347 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2348 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2349 printJob.setPrintable(alignPanel, pf);
\r
2351 if (printJob.printDialog())
\r
2357 catch (Exception PrintException)
\r
2359 PrintException.printStackTrace();
\r
2366 * Generates menu items and listener event actions for web service clients
\r
2369 public void BuildWebServiceMenu()
\r
2371 if ( (Discoverer.services != null)
\r
2372 && (Discoverer.services.size() > 0))
\r
2374 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2375 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2376 Vector wsmenu = new Vector();
\r
2377 if (msaws != null)
\r
2379 // Add any Multiple Sequence Alignment Services
\r
2380 final JMenu msawsmenu = new JMenu("Alignment");
\r
2381 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2383 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2385 final JMenuItem method = new JMenuItem(sh.getName());
\r
2386 method.addActionListener(new ActionListener()
\r
2388 public void actionPerformed(ActionEvent e)
\r
2390 SequenceI[] msa = gatherSequencesForAlignment();
\r
2391 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2392 false, true, viewport.getAlignment().getDataset());
\r
2397 msawsmenu.add(method);
\r
2398 // Deal with services that we know accept partial alignments.
\r
2399 if (sh.getName().indexOf("lustal") > -1)
\r
2401 // We know that ClustalWS can accept partial alignments for refinement.
\r
2402 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2403 methodR.addActionListener(new ActionListener()
\r
2405 public void actionPerformed(ActionEvent e)
\r
2407 SequenceI[] msa = gatherSequencesForAlignment();
\r
2408 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2409 true, true, viewport.getAlignment().getDataset());
\r
2414 msawsmenu.add(methodR);
\r
2418 wsmenu.add(msawsmenu);
\r
2420 if (secstrpr != null)
\r
2422 // Add any secondary structure prediction services
\r
2423 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2424 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2426 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2428 final JMenuItem method = new JMenuItem(sh.getName());
\r
2429 method.addActionListener(new ActionListener()
\r
2431 public void actionPerformed(ActionEvent e)
\r
2433 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2434 if (msa.length == 1)
\r
2436 // Single Sequence prediction
\r
2437 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2441 if (msa.length > 1)
\r
2443 // Single Sequence prediction
\r
2444 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2450 secstrmenu.add(method);
\r
2452 wsmenu.add(secstrmenu);
\r
2454 this.webService.removeAll();
\r
2455 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2457 webService.add( (JMenu) wsmenu.get(i));
\r
2462 this.webService.removeAll();
\r
2463 this.webService.add(this.webServiceNoServices);
\r
2465 // TODO: add in rediscovery function
\r
2466 // TODO: reduce code redundancy.
\r
2467 // TODO: group services by location as well as function.
\r
2470 public void vamsasStore_actionPerformed(ActionEvent e)
\r
2472 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2473 getProperty("LAST_DIRECTORY"));
\r
2475 chooser.setFileView(new JalviewFileView());
\r
2476 chooser.setDialogTitle("Export to Vamsas file");
\r
2477 chooser.setToolTipText("Export");
\r
2479 int value = chooser.showSaveDialog(this);
\r
2481 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2483 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2484 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
2485 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
2489 public void featureSettings_actionPerformed(ActionEvent e)
\r
2491 new FeatureSettings(viewport, alignPanel);
\r
2496 public void showTranslation_actionPerformed(ActionEvent e)
\r
2499 if(!viewport.alignment.isNucleotide())
\r
2502 viewport.showTranslation(showTranslation.isSelected());
\r
2504 if(!viewport.alignment.isNucleotide())
\r
2507 int s, sSize = viewport.alignment.getHeight();
\r
2508 SequenceI [] newSeq = new SequenceI[sSize];
\r
2511 StringBuffer protein;
\r
2513 for(s=0; s<sSize; s++)
\r
2515 protein = new StringBuffer();
\r
2516 seq = (SequenceI)viewport.alignment.getSequenceAt(s);
\r
2517 resSize = seq.getLength();
\r
2518 for(res = 0; res < resSize; res+=3)
\r
2520 String codon = seq.getSequence(res, res+3);
\r
2521 codon = codon.replace('U', 'T');
\r
2522 String aa = ResidueProperties.codonTranslate(codon);
\r
2524 protein.append(viewport.getGapCharacter());
\r
2525 else if(aa.equals("STOP"))
\r
2526 protein.append("X");
\r
2528 protein.append( aa );
\r
2530 newSeq[s] = new Sequence(seq.getName(), protein.toString());
\r
2534 AlignmentI al = new Alignment(newSeq);
\r
2535 al.setDataset(null);
\r
2538 ////////////////////////////////
\r
2539 // Copy annotations across
\r
2540 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2541 = viewport.alignment.getAlignmentAnnotation();
\r
2543 for (int i = 0; i < annotations.length; i++)
\r
2546 if (annotations[i].label.equals("Quality") ||
\r
2547 annotations[i].label.equals("Conservation") ||
\r
2548 annotations[i].label.equals("Consensus"))
\r
2554 aSize = viewport.alignment.getWidth()/3;
\r
2555 jalview.datamodel.Annotation [] anots =
\r
2556 new jalview.datamodel.Annotation[aSize];
\r
2558 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2560 if( annotations[i].annotations[a]==null
\r
2561 || annotations[i].annotations[a]==null)
\r
2564 anots[a/3] = new Annotation(
\r
2565 annotations[i].annotations[a].displayCharacter,
\r
2566 annotations[i].annotations[a].description,
\r
2567 annotations[i].annotations[a].secondaryStructure,
\r
2568 annotations[i].annotations[a].value,
\r
2569 annotations[i].annotations[a].colour);
\r
2572 jalview.datamodel.AlignmentAnnotation aa
\r
2573 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2574 annotations[i].description, anots );
\r
2575 al.addAnnotation(aa);
\r
2579 // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2580 // NEW_WINDOW_WIDTH,
\r
2581 // NEW_WINDOW_HEIGHT);
\r
2583 AlignViewport newViewport = new AlignViewport(al);
\r
2584 AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2585 tabbedPane.add("Protein", ap);
\r
2586 viewports.add(newViewport);
\r
2587 alignPanels.add(ap);
\r
2590 /////////////////////////
\r
2592 AlignViewport ds = new AlignViewport(al.getDataset());
\r
2593 ds.setDataset(true);
\r
2594 AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2595 tabbedPane.add("Dataset", dap);
\r
2596 viewports.add(ds);
\r
2597 alignPanels.add(dap);
\r
2598 /////////////////////////
\r
2603 public void tabSelected()
\r
2605 int index = tabbedPane.getSelectedIndex();
\r
2606 viewport = (AlignViewport)viewports.elementAt(index);
\r
2607 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r