2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Softwarechang
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import java.beans.*;
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26 import java.awt.datatransfer.*;
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27 import java.awt.event.*;
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28 import java.awt.print.*;
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29 import javax.swing.*;
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31 import jalview.analysis.*;
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32 import jalview.datamodel.*;
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33 import jalview.io.*;
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34 import jalview.jbgui.*;
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35 import jalview.schemes.*;
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36 import jalview.ws.*;
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37 import javax.swing.event.AncestorEvent;
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43 * @version $Revision$
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45 public class AlignFrame
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46 extends GAlignFrame implements ClipboardOwner
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48 /** DOCUMENT ME!! */
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49 public static final int NEW_WINDOW_WIDTH = 700;
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51 /** DOCUMENT ME!! */
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52 public static final int NEW_WINDOW_HEIGHT = 500;
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53 AlignmentPanel alignPanel;
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54 AlignViewport viewport;
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56 Vector viewports = new Vector();
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57 Vector alignPanels = new Vector();
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59 /** DOCUMENT ME!! */
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60 public String currentFileFormat = null;
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61 Stack historyList = new Stack();
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62 Stack redoList = new Stack();
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63 private int treeCount = 0;
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67 * Creates a new AlignFrame object.
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69 * @param al DOCUMENT ME!
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71 public AlignFrame(AlignmentI al)
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73 viewport = new AlignViewport(al);
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74 viewports.add(viewport);
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77 if(viewport.vconsensus==null)
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79 //Out of memory calculating consensus.
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80 BLOSUM62Colour.setEnabled(false);
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81 PIDColour.setEnabled(false);
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82 conservationMenuItem.setEnabled(false);
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83 modifyConservation.setEnabled(false);
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84 abovePIDThreshold.setEnabled(false);
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85 modifyPID.setEnabled(false);
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88 alignPanel = new AlignmentPanel(this, viewport);
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89 alignPanels.add(alignPanel);
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91 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
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93 if(sortby.equals("Id"))
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94 sortIDMenuItem_actionPerformed(null);
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95 else if(sortby.equals("Pairwise Identity"))
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96 sortPairwiseMenuItem_actionPerformed(null);
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98 // remove(tabbedPane);
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99 getContentPane().add(alignPanel, BorderLayout.CENTER);
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103 // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
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106 /////////////////////////
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107 if(al.getDataset()==null)
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109 al.setDataset(null);
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111 // AlignViewport ds = new AlignViewport(al.getDataset(), true);
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112 // AlignmentPanel dap = new AlignmentPanel(this, ds);
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113 // tabbedPane.add("Dataset", dap);
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114 // viewports.add(ds);
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115 // alignPanels.add(dap);
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116 /////////////////////////
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119 viewport.addPropertyChangeListener(new PropertyChangeListener()
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121 public void propertyChange(PropertyChangeEvent evt)
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123 if (evt.getPropertyName().equals("alignment"))
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125 alignmentChanged();
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131 if (Desktop.desktop != null)
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133 addServiceListeners();
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134 setGUINucleotide(al.isNucleotide());
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138 /* Set up intrinsic listeners for dynamically generated GUI bits. */
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139 private void addServiceListeners()
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141 final java.beans.PropertyChangeListener thisListener;
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142 // Do this once to get current state
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143 BuildWebServiceMenu();
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144 Desktop.discoverer.addPropertyChangeListener(
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145 thisListener = new java.beans.PropertyChangeListener()
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147 public void propertyChange(PropertyChangeEvent evt)
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149 // System.out.println("Discoverer property change.");
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150 if (evt.getPropertyName().equals("services"))
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152 // System.out.println("Rebuilding web service menu");
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153 BuildWebServiceMenu();
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157 addInternalFrameListener(new javax.swing.event.
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158 InternalFrameAdapter()
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160 public void internalFrameClosed(
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161 javax.swing.event.InternalFrameEvent evt)
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163 // System.out.println("deregistering discoverer listener");
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164 Desktop.discoverer.removePropertyChangeListener(thisListener);
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165 closeMenuItem_actionPerformed(null);
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172 public void setGUINucleotide(boolean nucleotide)
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174 showTranslation.setVisible( nucleotide );
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175 sequenceFeatures.setVisible(!nucleotide );
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176 featureSettings.setVisible( !nucleotide );
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177 conservationMenuItem.setVisible( !nucleotide );
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178 modifyConservation.setVisible( !nucleotide );
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180 //Deal with separators
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181 //Remember AlignFrame always starts as protein
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184 viewMenu.remove(viewMenu.getItemCount()-2);
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188 calculateMenu.remove(calculateMenu.getItemCount()-2);
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194 Added so Castor Mapping file can obtain Jalview Version
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196 public String getVersion()
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198 return jalview.bin.Cache.getProperty("VERSION");
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205 * @param String DOCUMENT ME!
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208 public void parseGroupsFile(String file)
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212 BufferedReader in = new BufferedReader(new FileReader(file));
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213 SequenceI seq = null;
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214 String line, type, desc, token;
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216 int index, start, end;
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217 StringTokenizer st;
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218 SequenceFeature sf;
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219 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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221 while ( (line = in.readLine()) != null)
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224 st = new StringTokenizer(line, "\t");
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225 if (st.countTokens() == 2)
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227 type = st.nextToken();
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228 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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229 fr.setColour(type, ucs.findColour("A"));
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233 while (st.hasMoreElements())
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235 desc = st.nextToken();
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236 token = st.nextToken();
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237 if (!token.equals("ID_NOT_SPECIFIED"))
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239 index = viewport.alignment.findIndex(viewport.alignment.findName(
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245 index = Integer.parseInt(st.nextToken());
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248 start = Integer.parseInt(st.nextToken());
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249 end = Integer.parseInt(st.nextToken());
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251 seq = viewport.alignment.getSequenceAt(index);
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252 start = seq.findIndex(start) - 1;
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253 end = seq.findIndex(end) - 1;
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255 type = st.nextToken();
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257 if (fr.getColour(type) == null)
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259 // Probably the old style groups file
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260 UserColourScheme ucs = new UserColourScheme(type);
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261 fr.setColour(type, ucs.findColour("A"));
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265 sf = new SequenceFeature(type, desc, "", start, end);
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267 seq.addSequenceFeature(sf);
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270 // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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271 // sg.addSequence(seq, false);
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273 // viewport.alignment.addGroup(sg);
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278 viewport.showSequenceFeatures = true;
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280 alignPanel.repaint();
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283 catch (Exception ex)
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285 System.out.println("Error parsing groups file: " + ex);
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289 public void fetchSequence_actionPerformed(ActionEvent e)
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291 new SequenceFetcher(this);
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298 * @param e DOCUMENT ME!
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300 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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302 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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307 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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312 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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313 }, currentFileFormat);
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315 chooser.setAcceptAllFileFilterUsed(false);
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316 chooser.setFileView(new JalviewFileView());
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317 chooser.setDialogTitle("Save Alignment to file");
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318 chooser.setToolTipText("Save");
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320 int value = chooser.showSaveDialog(this);
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322 if (value == JalviewFileChooser.APPROVE_OPTION)
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324 currentFileFormat = chooser.getSelectedFormat();
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326 if (currentFileFormat == null)
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328 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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329 "You must select a file format before saving!",
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330 "File format not specified",
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331 JOptionPane.WARNING_MESSAGE);
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332 value = chooser.showSaveDialog(this);
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336 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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337 currentFileFormat);
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339 String choice = chooser.getSelectedFile().getPath();
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340 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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342 saveAlignment(choice, currentFileFormat);
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346 public boolean saveAlignment(String file, String format)
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348 if (format.equalsIgnoreCase("Jalview"))
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350 String shortName = title;
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352 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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354 shortName = shortName.substring(shortName.lastIndexOf(
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355 java.io.File.separatorChar) + 1);
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358 Jalview2XML.SaveAlignment(this, file, shortName);
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360 // USE Jalview2XML to save this file
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365 String output = new FormatAdapter().formatSequences(format,
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366 viewport.getAlignment().
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368 if (output == null)
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375 java.io.PrintWriter out = new java.io.PrintWriter(
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376 new java.io.FileWriter(file));
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382 catch (Exception ex)
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384 ex.printStackTrace();
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393 * @param e DOCUMENT ME!
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395 protected void outputText_actionPerformed(ActionEvent e)
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397 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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398 Desktop.addInternalFrame(cap,
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399 "Alignment output - " + e.getActionCommand(), 600,
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401 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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402 viewport.getAlignment().
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409 * @param e DOCUMENT ME!
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411 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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413 new HTMLOutput(viewport,
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414 alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
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415 alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
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418 public void createImageMap(File file, String image)
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420 alignPanel.makePNGImageMap(file, image);
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426 * @param e DOCUMENT ME!
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428 public void createPNG(File f)
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430 alignPanel.makePNG(f);
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436 * @param e DOCUMENT ME!
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438 public void createEPS(File f)
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440 alignPanel.makeEPS(f);
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446 * @param e DOCUMENT ME!
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448 public void printMenuItem_actionPerformed(ActionEvent e)
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450 //Putting in a thread avoids Swing painting problems
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451 PrintThread thread = new PrintThread();
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458 * @param e DOCUMENT ME!
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460 public void closeMenuItem_actionPerformed(ActionEvent e)
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464 PaintRefresher.components.remove(viewport.alignment);
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465 this.setClosed(true);
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467 catch (Exception ex)
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475 void updateEditMenuBar()
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477 if (historyList.size() > 0)
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479 undoMenuItem.setEnabled(true);
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481 HistoryItem hi = (HistoryItem) historyList.peek();
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482 undoMenuItem.setText("Undo " + hi.getDescription());
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486 undoMenuItem.setEnabled(false);
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487 undoMenuItem.setText("Undo");
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490 if (redoList.size() > 0)
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492 redoMenuItem.setEnabled(true);
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494 HistoryItem hi = (HistoryItem) redoList.peek();
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495 redoMenuItem.setText("Redo " + hi.getDescription());
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499 redoMenuItem.setEnabled(false);
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500 redoMenuItem.setText("Redo");
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507 * @param hi DOCUMENT ME!
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509 public void addHistoryItem(HistoryItem hi)
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511 historyList.push(hi);
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512 updateEditMenuBar();
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518 * @param e DOCUMENT ME!
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520 protected void undoMenuItem_actionPerformed(ActionEvent e)
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522 HistoryItem hi = (HistoryItem) historyList.pop();
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523 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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524 HistoryItem.HIDE));
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525 restoreHistoryItem(hi);
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526 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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532 * @param e DOCUMENT ME!
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534 protected void redoMenuItem_actionPerformed(ActionEvent e)
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536 HistoryItem hi = (HistoryItem) redoList.pop();
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537 restoreHistoryItem(hi);
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538 updateEditMenuBar();
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539 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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542 // used by undo and redo
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543 void restoreHistoryItem(HistoryItem hi)
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545 if (hi.getType() == HistoryItem.SORT)
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547 for (int i = 0; i < hi.getSequences().size(); i++)
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549 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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556 for (int i = 0; i < hi.getSequences().size(); i++)
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558 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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560 if (restore.getLength() == 0)
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562 restore.setSequence(hi.getHidden().elementAt(i).toString());
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563 viewport.alignment.getSequences().insertElementAt(restore,
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564 hi.getAlignIndex(i));
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568 restore.setSequence(hi.getHidden().elementAt(i).toString());
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572 if (hi.getType() == HistoryItem.PASTE)
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574 for (int i = viewport.alignment.getHeight() - 1;
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575 i > (hi.getSequences().size() - 1); i--)
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577 viewport.alignment.deleteSequence(i);
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582 updateEditMenuBar();
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584 viewport.firePropertyChange("alignment", null,
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585 viewport.getAlignment().getSequences());
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591 * @param up DOCUMENT ME!
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593 public void moveSelectedSequences(boolean up)
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595 SequenceGroup sg = viewport.getSelectionGroup();
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604 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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606 SequenceI seq = viewport.alignment.getSequenceAt(i);
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608 if (!sg.sequences.contains(seq))
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613 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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615 if (sg.sequences.contains(temp))
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620 viewport.alignment.getSequences().setElementAt(temp, i);
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621 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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626 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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628 SequenceI seq = viewport.alignment.getSequenceAt(i);
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630 if (!sg.sequences.contains(seq))
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635 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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637 if (sg.sequences.contains(temp))
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642 viewport.alignment.getSequences().setElementAt(temp, i);
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643 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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647 alignPanel.repaint();
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650 public void lostOwnership(Clipboard clipboard, Transferable contents)
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652 Desktop.jalviewClipboard = null;
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659 * @param e DOCUMENT ME!
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661 protected void copy_actionPerformed(ActionEvent e)
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663 if (viewport.getSelectionGroup() == null)
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668 SequenceGroup sg = viewport.getSelectionGroup();
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670 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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672 Hashtable orderedSeqs = new Hashtable();
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673 SequenceI[] seqs = new SequenceI[sg.getSize()];
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675 for (int i = 0; i < sg.getSize(); i++)
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677 SequenceI seq = sg.getSequenceAt(i);
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678 int index = viewport.alignment.findIndex(seq);
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679 orderedSeqs.put(index + "", seq);
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682 int index = 0, startRes, endRes;
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685 for (int i = 0; i < sg.getSize(); i++)
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687 SequenceI seq = null;
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689 while (seq == null)
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691 if (orderedSeqs.containsKey(index + ""))
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693 seq = (SequenceI) orderedSeqs.get(index + "");
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705 //Returns residue following index if gap
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706 startRes = seq.findPosition(sg.getStartRes());
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709 //Need to find the residue preceeding index if gap
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712 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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714 ch = seq.getCharAt(j);
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715 if (!jalview.util.Comparison.isGap( (ch)))
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723 endRes += seq.getStart() - 1;
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726 seqs[i] = new Sequence(seq.getName(),
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727 seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
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730 seqs[i].setDescription(seq.getDescription());
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731 seqs[i].setDBRef(seq.getDBRef());
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732 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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733 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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737 FastaFile ff = new FastaFile();
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738 ff.addJVSuffix( viewport.showJVSuffix );
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739 c.setContents(new StringSelection( ff.print(seqs)), this);
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740 Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};
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746 * @param e DOCUMENT ME!
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748 protected void pasteNew_actionPerformed(ActionEvent e)
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756 * @param e DOCUMENT ME!
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758 protected void pasteThis_actionPerformed(ActionEvent e)
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760 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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761 HistoryItem.PASTE));
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768 * @param newAlignment DOCUMENT ME!
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770 void paste(boolean newAlignment)
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774 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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775 Transferable contents = c.getContents(this);
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777 if (contents == null)
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782 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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786 String format = IdentifyFile.Identify(str, "Paste");
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787 SequenceI[] sequences;
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789 if(Desktop.jalviewClipboard!=null)
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791 // The clipboard was filled from within Jalview, we must use the sequences
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792 // And dataset from the copied alignment
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793 sequences = (SequenceI[])Desktop.jalviewClipboard[0];
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797 sequences = new FormatAdapter().readFile(str, "Paste", format);
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803 Alignment alignment = new Alignment(sequences);
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805 if(Desktop.jalviewClipboard!=null)
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806 alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
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808 alignment.setDataset( null );
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811 AlignFrame af = new AlignFrame(alignment);
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812 String newtitle = new String("Copied sequences");
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814 if (title.startsWith("Copied sequences"))
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820 newtitle = newtitle.concat("- from " + title);
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823 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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824 NEW_WINDOW_HEIGHT);
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829 for (int i = 0; i < sequences.length; i++)
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831 viewport.alignment.addSequence(sequences[i]);
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832 if(sequences[i].getDatasetSequence()==null)
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834 ////////////////////////////
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835 //Datset needs extension;
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836 /////////////////////////////
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837 Sequence ds = new Sequence(sequences[i].getName(),
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838 AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
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839 sequences[i].getStart(),
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840 sequences[i].getEnd());
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841 sequences[i].setDatasetSequence(ds);
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842 viewport.alignment.getDataset().addSequence(ds);
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848 viewport.setEndSeq(viewport.alignment.getHeight());
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849 viewport.alignment.getWidth();
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850 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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853 catch (Exception ex)
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855 // could be anything being pasted in here
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864 * @param e DOCUMENT ME!
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866 protected void cut_actionPerformed(ActionEvent e)
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868 copy_actionPerformed(null);
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869 delete_actionPerformed(null);
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875 * @param e DOCUMENT ME!
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877 protected void delete_actionPerformed(ActionEvent e)
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880 if (viewport.getSelectionGroup() == null)
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885 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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886 HistoryItem.HIDE));
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888 SequenceGroup sg = viewport.getSelectionGroup();
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889 boolean allSequences = false;
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890 if (sg.sequences.size() == viewport.alignment.getHeight())
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892 allSequences = true;
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895 for (int i = 0; i < sg.sequences.size(); i++)
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897 SequenceI seq = sg.getSequenceAt(i);
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898 int index = viewport.getAlignment().findIndex(seq);
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899 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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901 // If the cut affects all sequences, remove highlighted columns
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904 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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905 sg.getEndRes() + 1);
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908 if (seq.getSequence().length() < 1)
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910 viewport.getAlignment().deleteSequence(seq);
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914 viewport.getAlignment().getSequences().setElementAt(seq, index);
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918 viewport.setSelectionGroup(null);
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919 viewport.alignment.deleteGroup(sg);
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921 viewport.firePropertyChange("alignment", null,
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922 viewport.getAlignment().getSequences());
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926 if (viewport.getAlignment().getHeight() < 1)
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930 this.setClosed(true);
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932 catch (Exception ex)
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941 * @param e DOCUMENT ME!
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943 protected void deleteGroups_actionPerformed(ActionEvent e)
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945 viewport.alignment.deleteAllGroups();
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946 viewport.setSelectionGroup(null);
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947 alignPanel.repaint();
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953 * @param e DOCUMENT ME!
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955 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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957 SequenceGroup sg = new SequenceGroup();
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959 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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962 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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965 sg.setEndRes(viewport.alignment.getWidth() - 1);
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966 viewport.setSelectionGroup(sg);
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967 PaintRefresher.Refresh(null, viewport.alignment);
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973 * @param e DOCUMENT ME!
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975 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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977 viewport.setSelectionGroup(null);
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978 viewport.getColumnSelection().clear();
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979 viewport.setSelectionGroup(null);
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980 alignPanel.annotationPanel.activeRes = null;
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981 PaintRefresher.Refresh(null, viewport.alignment);
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987 * @param e DOCUMENT ME!
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989 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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991 SequenceGroup sg = viewport.getSelectionGroup();
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995 selectAllSequenceMenuItem_actionPerformed(null);
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1000 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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1003 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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1006 PaintRefresher.Refresh(null, viewport.alignment);
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1012 * @param e DOCUMENT ME!
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1014 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1016 ColumnSelection colSel = viewport.getColumnSelection();
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1018 if (colSel.size() > 0)
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1020 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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1021 HistoryItem.HIDE));
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1023 int min = colSel.getMin();
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1024 viewport.getAlignment().trimLeft(min);
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1025 colSel.compensateForEdit(0, min);
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1027 if (viewport.getSelectionGroup() != null)
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1029 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1032 Vector groups = viewport.alignment.getGroups();
\r
1034 for (int i = 0; i < groups.size(); i++)
\r
1036 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1038 if (!sg.adjustForRemoveLeft(min))
\r
1040 viewport.alignment.deleteGroup(sg);
\r
1044 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1051 * @param e DOCUMENT ME!
\r
1053 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1055 ColumnSelection colSel = viewport.getColumnSelection();
\r
1057 if (colSel.size() > 0)
\r
1059 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1060 HistoryItem.HIDE));
\r
1062 int max = colSel.getMax();
\r
1063 viewport.getAlignment().trimRight(max);
\r
1065 if (viewport.getSelectionGroup() != null)
\r
1067 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1070 Vector groups = viewport.alignment.getGroups();
\r
1072 for (int i = 0; i < groups.size(); i++)
\r
1074 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1076 if (!sg.adjustForRemoveRight(max))
\r
1078 viewport.alignment.deleteGroup(sg);
\r
1082 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1089 * @param e DOCUMENT ME!
\r
1091 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1093 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1094 viewport.alignment, HistoryItem.HIDE));
\r
1096 //This is to maintain viewport position on first residue
\r
1097 //of first sequence
\r
1098 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1099 int startRes = seq.findPosition(viewport.startRes);
\r
1101 viewport.getAlignment().removeGaps();
\r
1103 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1105 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1111 * @param e DOCUMENT ME!
\r
1113 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1115 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1116 HistoryItem.HIDE));
\r
1118 //This is to maintain viewport position on first residue
\r
1119 //of first sequence
\r
1120 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1121 int startRes = seq.findPosition(viewport.startRes);
\r
1124 SequenceI current;
\r
1127 Vector seqs = null;
\r
1130 int end = viewport.alignment.getWidth();
\r
1132 if (viewport.getSelectionGroup() != null
\r
1133 && viewport.getSelectionGroup().sequences != null
\r
1134 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1136 seqs = viewport.getSelectionGroup().sequences;
\r
1137 start = viewport.getSelectionGroup().getStartRes();
\r
1138 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1142 seqs = viewport.alignment.getSequences();
\r
1145 for (int i = 0; i < seqs.size(); i++)
\r
1147 current = (SequenceI) seqs.elementAt(i);
\r
1148 jSize = current.getLength();
\r
1150 // Removing a range is much quicker than removing gaps
\r
1151 // one by one for long sequences
\r
1153 int rangeStart=-1, rangeEnd=-1;
\r
1157 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1159 if(rangeStart==-1)
\r
1174 current.deleteChars(rangeStart, rangeEnd);
\r
1175 j-=rangeEnd-rangeStart;
\r
1176 jSize-=rangeEnd-rangeStart;
\r
1184 while (j < end && j < jSize);
\r
1187 current.deleteChars(rangeStart, rangeEnd);
\r
1191 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1193 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1196 public void alignmentChanged()
\r
1198 if(viewport.vconsensus!=null)
\r
1200 viewport.updateConsensus();
\r
1201 viewport.updateConservation();
\r
1203 resetAllColourSchemes();
\r
1204 if(alignPanel.overviewPanel!=null)
\r
1205 alignPanel.overviewPanel.updateOverviewImage();
\r
1207 Provenance prov = viewport.alignment.getProvenance();
\r
1210 prov = new Provenance();
\r
1211 viewport.alignment.setProvenance(prov);
\r
1214 prov.addEntry("Me",
\r
1215 "Edited in Jalview", new java.util.Date(), "myID");
\r
1217 alignPanel.repaint();
\r
1220 void resetAllColourSchemes()
\r
1222 ColourSchemeI cs = viewport.globalColourScheme;
\r
1225 if (cs instanceof ClustalxColourScheme)
\r
1227 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1228 resetClustalX(viewport.alignment.getSequences(),
\r
1229 viewport.alignment.getWidth());
\r
1232 cs.setConsensus(viewport.vconsensus);
\r
1233 if (cs.conservationApplied())
\r
1235 Alignment al = (Alignment) viewport.alignment;
\r
1236 Conservation c = new Conservation("All",
\r
1237 ResidueProperties.propHash, 3,
\r
1238 al.getSequences(), 0,
\r
1239 al.getWidth() - 1);
\r
1241 c.verdict(false, viewport.ConsPercGaps);
\r
1243 cs.setConservation(c);
\r
1247 int s, sSize = viewport.alignment.getGroups().size();
\r
1248 for(s=0; s<sSize; s++)
\r
1250 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1251 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1253 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1255 sg.recalcConservation();
\r
1262 * @param e DOCUMENT ME!
\r
1264 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1266 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1267 HistoryItem.HIDE));
\r
1269 SequenceI current;
\r
1270 int Width = viewport.getAlignment().getWidth();
\r
1272 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1275 current = viewport.getAlignment().getSequenceAt(i);
\r
1277 if (current.getLength() < Width)
\r
1279 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1283 alignmentChanged();
\r
1289 * @param e DOCUMENT ME!
\r
1291 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1293 JInternalFrame frame = new JInternalFrame();
\r
1294 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1295 frame.setContentPane(finder);
\r
1296 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1297 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1303 * @param e DOCUMENT ME!
\r
1305 public void font_actionPerformed(ActionEvent e)
\r
1307 new FontChooser(alignPanel);
\r
1313 * @param e DOCUMENT ME!
\r
1315 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1317 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1319 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1320 alignPanel.repaint();
\r
1327 * @param e DOCUMENT ME!
\r
1329 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1331 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1332 alignPanel.repaint();
\r
1338 * @param e DOCUMENT ME!
\r
1340 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1342 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1343 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1344 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1345 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1346 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1347 alignPanel.repaint();
\r
1353 * @param e DOCUMENT ME!
\r
1355 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1357 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1358 alignPanel.repaint();
\r
1364 * @param e DOCUMENT ME!
\r
1366 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1368 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1369 alignPanel.repaint();
\r
1375 * @param e DOCUMENT ME!
\r
1377 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1379 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1380 alignPanel.repaint();
\r
1386 * @param e DOCUMENT ME!
\r
1388 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1390 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1391 alignPanel.repaint();
\r
1397 * @param e DOCUMENT ME!
\r
1399 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1401 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1402 alignPanel.repaint();
\r
1408 * @param e DOCUMENT ME!
\r
1410 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1412 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1413 alignPanel.repaint();
\r
1419 * @param evt DOCUMENT ME!
\r
1421 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1423 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1425 if (viewport.showSequenceFeatures)
\r
1427 new SequenceFeatureFetcher(viewport.
\r
1432 featureSettings.setEnabled(true);
\r
1434 alignPanel.repaint();
\r
1440 * @param e DOCUMENT ME!
\r
1442 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1444 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1445 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1451 * @param e DOCUMENT ME!
\r
1453 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1455 if (alignPanel.overviewPanel != null)
\r
1460 JInternalFrame frame = new JInternalFrame();
\r
1461 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1462 frame.setContentPane(overview);
\r
1463 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1464 frame.getWidth(), frame.getHeight());
\r
1466 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1467 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1469 public void internalFrameClosed(
\r
1470 javax.swing.event.InternalFrameEvent evt)
\r
1472 alignPanel.setOverviewPanel(null);
\r
1477 alignPanel.setOverviewPanel(overview);
\r
1483 * @param e DOCUMENT ME!
\r
1485 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1487 changeColour(null);
\r
1493 * @param e DOCUMENT ME!
\r
1495 public void clustalColour_actionPerformed(ActionEvent e)
\r
1497 changeColour(new ClustalxColourScheme(
\r
1498 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1504 * @param e DOCUMENT ME!
\r
1506 public void zappoColour_actionPerformed(ActionEvent e)
\r
1508 changeColour(new ZappoColourScheme());
\r
1514 * @param e DOCUMENT ME!
\r
1516 public void taylorColour_actionPerformed(ActionEvent e)
\r
1518 changeColour(new TaylorColourScheme());
\r
1524 * @param e DOCUMENT ME!
\r
1526 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1528 changeColour(new HydrophobicColourScheme());
\r
1534 * @param e DOCUMENT ME!
\r
1536 public void helixColour_actionPerformed(ActionEvent e)
\r
1538 changeColour(new HelixColourScheme());
\r
1544 * @param e DOCUMENT ME!
\r
1546 public void strandColour_actionPerformed(ActionEvent e)
\r
1548 changeColour(new StrandColourScheme());
\r
1554 * @param e DOCUMENT ME!
\r
1556 public void turnColour_actionPerformed(ActionEvent e)
\r
1558 changeColour(new TurnColourScheme());
\r
1564 * @param e DOCUMENT ME!
\r
1566 public void buriedColour_actionPerformed(ActionEvent e)
\r
1568 changeColour(new BuriedColourScheme());
\r
1574 * @param e DOCUMENT ME!
\r
1576 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1578 changeColour(new NucleotideColourScheme());
\r
1584 * @param e DOCUMENT ME!
\r
1586 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1588 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1594 * @param cs DOCUMENT ME!
\r
1596 void changeColour(ColourSchemeI cs)
\r
1598 int threshold = 0;
\r
1602 if (viewport.getAbovePIDThreshold())
\r
1604 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1607 cs.setThreshold(threshold,
\r
1608 viewport.getIgnoreGapsConsensus());
\r
1610 viewport.setGlobalColourScheme(cs);
\r
1614 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1617 if (viewport.getConservationSelected())
\r
1620 Alignment al = (Alignment) viewport.alignment;
\r
1621 Conservation c = new Conservation("All",
\r
1622 ResidueProperties.propHash, 3,
\r
1623 al.getSequences(), 0,
\r
1624 al.getWidth() - 1);
\r
1627 c.verdict(false, viewport.ConsPercGaps);
\r
1629 cs.setConservation(c);
\r
1631 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1636 cs.setConservation(null);
\r
1639 cs.setConsensus(viewport.vconsensus);
\r
1642 viewport.setGlobalColourScheme(cs);
\r
1644 if (viewport.getColourAppliesToAllGroups())
\r
1646 Vector groups = viewport.alignment.getGroups();
\r
1648 for (int i = 0; i < groups.size(); i++)
\r
1650 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1658 if (cs instanceof ClustalxColourScheme)
\r
1660 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1662 else if (cs instanceof UserColourScheme)
\r
1664 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1670 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1672 catch (Exception ex)
\r
1677 if (viewport.getAbovePIDThreshold()
\r
1678 || cs instanceof PIDColourScheme
\r
1679 || cs instanceof Blosum62ColourScheme)
\r
1681 sg.cs.setThreshold(threshold,
\r
1682 viewport.getIgnoreGapsConsensus());
\r
1684 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1688 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1691 if (viewport.getConservationSelected())
\r
1693 Conservation c = new Conservation("Group",
\r
1694 ResidueProperties.propHash, 3,
\r
1696 viewport.alignment.getWidth() - 1);
\r
1698 c.verdict(false, viewport.ConsPercGaps);
\r
1699 sg.cs.setConservation(c);
\r
1702 sg.cs.setConservation(null);
\r
1706 if (alignPanel.getOverviewPanel() != null)
\r
1708 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1711 alignPanel.repaint();
\r
1717 * @param e DOCUMENT ME!
\r
1719 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1721 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1723 SliderPanel.setPIDSliderSource(alignPanel,
\r
1724 viewport.getGlobalColourScheme(),
\r
1726 SliderPanel.showPIDSlider();
\r
1733 * @param e DOCUMENT ME!
\r
1735 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1737 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1739 SliderPanel.setConservationSlider(alignPanel,
\r
1740 viewport.globalColourScheme,
\r
1742 SliderPanel.showConservationSlider();
\r
1749 * @param e DOCUMENT ME!
\r
1751 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1753 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1755 viewport.setAbovePIDThreshold(false);
\r
1756 abovePIDThreshold.setSelected(false);
\r
1758 changeColour(viewport.getGlobalColourScheme());
\r
1760 modifyConservation_actionPerformed(null);
\r
1766 * @param e DOCUMENT ME!
\r
1768 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1770 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1772 conservationMenuItem.setSelected(false);
\r
1773 viewport.setConservationSelected(false);
\r
1775 changeColour(viewport.getGlobalColourScheme());
\r
1777 modifyPID_actionPerformed(null);
\r
1783 * @param e DOCUMENT ME!
\r
1785 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1787 if (e.getActionCommand().equals("User Defined..."))
\r
1789 new UserDefinedColours(alignPanel, null);
\r
1793 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1794 getUserColourSchemes().get(e.getActionCommand());
\r
1796 changeColour(udc);
\r
1800 public void updateUserColourMenu()
\r
1803 Component[] menuItems = colourMenu.getMenuComponents();
\r
1804 int i, iSize = menuItems.length;
\r
1805 for (i = 0; i < iSize; i++)
\r
1807 if (menuItems[i].getName() != null &&
\r
1808 menuItems[i].getName().equals("USER_DEFINED"))
\r
1810 colourMenu.remove(menuItems[i]);
\r
1814 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1816 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1817 getUserColourSchemes().keys();
\r
1819 while (userColours.hasMoreElements())
\r
1821 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1822 nextElement().toString());
\r
1823 radioItem.setName("USER_DEFINED");
\r
1824 radioItem.addMouseListener(new MouseAdapter()
\r
1826 public void mousePressed(MouseEvent evt)
\r
1828 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1830 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1832 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1833 "Remove from default list?",
\r
1834 "Remove user defined colour",
\r
1835 JOptionPane.YES_NO_OPTION);
\r
1836 if(option == JOptionPane.YES_OPTION)
\r
1838 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1839 colourMenu.remove(radioItem);
\r
1842 radioItem.addActionListener(new ActionListener()
\r
1844 public void actionPerformed(ActionEvent evt)
\r
1846 userDefinedColour_actionPerformed(evt);
\r
1852 radioItem.addActionListener(new ActionListener()
\r
1854 public void actionPerformed(ActionEvent evt)
\r
1856 userDefinedColour_actionPerformed(evt);
\r
1860 colourMenu.insert(radioItem, 15);
\r
1861 colours.add(radioItem);
\r
1869 * @param e DOCUMENT ME!
\r
1871 public void PIDColour_actionPerformed(ActionEvent e)
\r
1873 changeColour(new PIDColourScheme());
\r
1879 * @param e DOCUMENT ME!
\r
1881 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1883 changeColour(new Blosum62ColourScheme());
\r
1889 * @param e DOCUMENT ME!
\r
1891 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1893 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1894 HistoryItem.SORT));
\r
1895 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1896 viewport.getAlignment().getSequenceAt(0));
\r
1897 alignPanel.repaint();
\r
1903 * @param e DOCUMENT ME!
\r
1905 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1907 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1908 HistoryItem.SORT));
\r
1909 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1910 alignPanel.repaint();
\r
1916 * @param e DOCUMENT ME!
\r
1918 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1920 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1921 HistoryItem.SORT));
\r
1923 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1924 alignPanel.repaint();
\r
1930 * @param e DOCUMENT ME!
\r
1932 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1934 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1935 JInternalFrame frame = new JInternalFrame();
\r
1936 frame.setContentPane(sp);
\r
1937 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1944 * @param e DOCUMENT ME!
\r
1946 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1948 if ( (viewport.getSelectionGroup() == null) ||
\r
1949 (viewport.getSelectionGroup().getSize() < 2))
\r
1951 JOptionPane.showInternalMessageDialog(this,
\r
1952 "You must select at least 2 sequences.",
\r
1953 "Invalid Selection",
\r
1954 JOptionPane.WARNING_MESSAGE);
\r
1958 JInternalFrame frame = new JInternalFrame();
\r
1959 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1960 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1967 * @param e DOCUMENT ME!
\r
1969 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1971 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1972 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1973 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1974 (viewport.getAlignment().getHeight() < 4))
\r
1976 JOptionPane.showInternalMessageDialog(this,
\r
1977 "Principal component analysis must take\n" +
\r
1978 "at least 4 input sequences.",
\r
1979 "Sequence selection insufficient",
\r
1980 JOptionPane.WARNING_MESSAGE);
\r
1985 new PCAPanel(viewport);
\r
1991 * @param e DOCUMENT ME!
\r
1993 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1995 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
2001 * @param e DOCUMENT ME!
\r
2003 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
2005 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2011 * @param e DOCUMENT ME!
\r
2013 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2015 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2021 * @param e DOCUMENT ME!
\r
2023 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2025 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2031 * @param type DOCUMENT ME!
\r
2032 * @param pwType DOCUMENT ME!
\r
2033 * @param title DOCUMENT ME!
\r
2035 void NewTreePanel(String type, String pwType, String title)
\r
2037 final TreePanel tp;
\r
2039 if ( (viewport.getSelectionGroup() != null) &&
\r
2040 (viewport.getSelectionGroup().getSize() > 3))
\r
2043 SequenceGroup sg = viewport.getSelectionGroup();
\r
2045 /* Decide if the selection is a column region */
\r
2046 while (s < sg.sequences.size())
\r
2048 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2051 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2052 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2053 "Try using the Pad function in the edit menu,\n" +
\r
2054 "or one of the multiple sequence alignment web services.",
\r
2055 "Sequences in selection are not aligned",
\r
2056 JOptionPane.WARNING_MESSAGE);
\r
2062 title = title + " on region";
\r
2063 tp = new TreePanel(viewport,
\r
2064 viewport.getSelectionGroup().sequences, type, pwType,
\r
2065 sg.getStartRes(), sg.getEndRes());
\r
2069 //are the sequences aligned?
\r
2070 if (!viewport.alignment.isAligned())
\r
2072 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2073 "The sequences must be aligned before creating a tree.\n" +
\r
2074 "Try using the Pad function in the edit menu,\n" +
\r
2075 "or one of the multiple sequence alignment web services.",
\r
2076 "Sequences not aligned",
\r
2077 JOptionPane.WARNING_MESSAGE);
\r
2082 tp = new TreePanel(viewport,
\r
2083 viewport.getAlignment().getSequences(), type, pwType,
\r
2085 viewport.alignment.getWidth());
\r
2088 addTreeMenuItem(tp, title);
\r
2089 viewport.setCurrentTree(tp.getTree());
\r
2091 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2097 * @param title DOCUMENT ME!
\r
2098 * @param order DOCUMENT ME!
\r
2100 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2102 final JMenuItem item = new JMenuItem("by " + title);
\r
2104 item.addActionListener(new java.awt.event.ActionListener()
\r
2106 public void actionPerformed(ActionEvent e)
\r
2108 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2109 HistoryItem.SORT));
\r
2111 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2112 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2113 alignPanel.repaint();
\r
2119 * Maintain the Order by->Displayed Tree menu.
\r
2120 * Creates a new menu item for a TreePanel with an appropriate
\r
2121 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2122 * to remove the menu item when the treePanel is closed, and adjust
\r
2123 * the tree leaf to sequence mapping when the alignment is modified.
\r
2124 * @param treePanel Displayed tree window.
\r
2125 * @param title SortBy menu item title.
\r
2127 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2129 final JMenuItem item = new JMenuItem(title);
\r
2133 if (treeCount == 1)
\r
2135 sort.add(sortByTreeMenu);
\r
2138 sortByTreeMenu.add(item);
\r
2139 item.addActionListener(new java.awt.event.ActionListener()
\r
2141 public void actionPerformed(ActionEvent e)
\r
2143 addHistoryItem(new HistoryItem("Tree Sort",
\r
2144 viewport.alignment, HistoryItem.SORT));
\r
2145 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2146 treePanel.getTree());
\r
2147 alignPanel.repaint();
\r
2151 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2152 InternalFrameAdapter()
\r
2154 public void internalFrameClosed(
\r
2155 javax.swing.event.InternalFrameEvent evt)
\r
2158 sortByTreeMenu.remove(item);
\r
2160 if (treeCount == 0)
\r
2162 sort.remove(sortByTreeMenu);
\r
2170 * Work out whether the whole set of sequences
\r
2171 * or just the selected set will be submitted for multiple alignment.
\r
2174 private SequenceI[] gatherSequencesForAlignment()
\r
2176 // Now, check we have enough sequences
\r
2177 SequenceI[] msa = null;
\r
2179 if ( (viewport.getSelectionGroup() != null) &&
\r
2180 (viewport.getSelectionGroup().getSize() > 1))
\r
2182 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2183 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2185 msa = new SequenceI[sz = seqs.getSize()];
\r
2187 for (int i = 0; i < sz; i++)
\r
2189 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2194 Vector seqs = viewport.getAlignment().getSequences();
\r
2196 if (seqs.size() > 1)
\r
2198 msa = new SequenceI[seqs.size()];
\r
2200 for (int i = 0; i < seqs.size(); i++)
\r
2202 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2210 * Decides what is submitted to a secondary structure prediction service,
\r
2211 * the currently selected sequence, or the currently selected alignment
\r
2212 * (where the first sequence in the set is the one that the prediction
\r
2215 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2217 SequenceI seq = null;
\r
2218 SequenceI[] msa = null;
\r
2220 if ( (viewport.getSelectionGroup() != null) &&
\r
2221 (viewport.getSelectionGroup().getSize() > 0))
\r
2223 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2224 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2226 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2228 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2233 msa = new SequenceI[sz = seqs.getSize()];
\r
2235 for (int i = 0; i < sz; i++)
\r
2237 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2243 Vector seqs = viewport.getAlignment().getSequences();
\r
2245 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2247 seq = (SequenceI) seqs.elementAt(0);
\r
2251 msa = new SequenceI[seqs.size()];
\r
2253 for (int i = 0; i < seqs.size(); i++)
\r
2255 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2267 return new SequenceI[]
\r
2277 * @param e DOCUMENT ME!
\r
2279 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2281 // Pick the tree file
\r
2282 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2284 "LAST_DIRECTORY"));
\r
2285 chooser.setFileView(new JalviewFileView());
\r
2286 chooser.setDialogTitle("Select a newick-like tree file");
\r
2287 chooser.setToolTipText("Load a tree file");
\r
2289 int value = chooser.showOpenDialog(null);
\r
2291 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2293 String choice = chooser.getSelectedFile().getPath();
\r
2294 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2298 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2300 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2302 catch (Exception ex)
\r
2304 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2305 "Problem reading tree file",
\r
2307 JOptionPane.WARNING_MESSAGE);
\r
2308 ex.printStackTrace();
\r
2314 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2316 return ShowNewickTree(nf,title,600,500,4,5);
\r
2321 * @param nf DOCUMENT ME!
\r
2322 * @param title DOCUMENT ME!
\r
2324 * @return DOCUMENT ME!
\r
2326 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2328 TreePanel tp = null;
\r
2334 if (nf.getTree() != null)
\r
2336 tp = new TreePanel(viewport,
\r
2337 viewport.getAlignment().getSequences(), nf,
\r
2344 tp.setLocation(x,y);
\r
2347 Desktop.addInternalFrame(tp, title, w, h);
\r
2348 addTreeMenuItem(tp, title);
\r
2351 catch (Exception ex)
\r
2353 ex.printStackTrace();
\r
2364 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2365 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2366 printJob.setPrintable(alignPanel, pf);
\r
2368 if (printJob.printDialog())
\r
2374 catch (Exception PrintException)
\r
2376 PrintException.printStackTrace();
\r
2383 * Generates menu items and listener event actions for web service clients
\r
2386 public void BuildWebServiceMenu()
\r
2388 if ( (Discoverer.services != null)
\r
2389 && (Discoverer.services.size() > 0))
\r
2391 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2392 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2393 Vector wsmenu = new Vector();
\r
2394 if (msaws != null)
\r
2396 // Add any Multiple Sequence Alignment Services
\r
2397 final JMenu msawsmenu = new JMenu("Alignment");
\r
2398 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2400 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2402 final JMenuItem method = new JMenuItem(sh.getName());
\r
2403 method.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 false, true, viewport.getAlignment().getDataset());
\r
2414 msawsmenu.add(method);
\r
2415 // Deal with services that we know accept partial alignments.
\r
2416 if (sh.getName().indexOf("lustal") > -1)
\r
2418 // We know that ClustalWS can accept partial alignments for refinement.
\r
2419 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2420 methodR.addActionListener(new ActionListener()
\r
2422 public void actionPerformed(ActionEvent e)
\r
2424 SequenceI[] msa = gatherSequencesForAlignment();
\r
2425 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2426 true, true, viewport.getAlignment().getDataset());
\r
2431 msawsmenu.add(methodR);
\r
2435 wsmenu.add(msawsmenu);
\r
2437 if (secstrpr != null)
\r
2439 // Add any secondary structure prediction services
\r
2440 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2441 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2443 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2445 final JMenuItem method = new JMenuItem(sh.getName());
\r
2446 method.addActionListener(new ActionListener()
\r
2448 public void actionPerformed(ActionEvent e)
\r
2450 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2451 if (msa.length == 1)
\r
2453 // Single Sequence prediction
\r
2454 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2458 if (msa.length > 1)
\r
2460 // Single Sequence prediction
\r
2461 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2467 secstrmenu.add(method);
\r
2469 wsmenu.add(secstrmenu);
\r
2471 this.webService.removeAll();
\r
2472 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2474 webService.add( (JMenu) wsmenu.get(i));
\r
2479 this.webService.removeAll();
\r
2480 this.webService.add(this.webServiceNoServices);
\r
2482 // TODO: add in rediscovery function
\r
2483 // TODO: reduce code redundancy.
\r
2484 // TODO: group services by location as well as function.
\r
2487 /* public void vamsasStore_actionPerformed(ActionEvent e)
\r
2489 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2490 getProperty("LAST_DIRECTORY"));
\r
2492 chooser.setFileView(new JalviewFileView());
\r
2493 chooser.setDialogTitle("Export to Vamsas file");
\r
2494 chooser.setToolTipText("Export");
\r
2496 int value = chooser.showSaveDialog(this);
\r
2498 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2500 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2501 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
2502 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
2506 public void featureSettings_actionPerformed(ActionEvent e)
\r
2508 new FeatureSettings(viewport, alignPanel);
\r
2513 public void showTranslation_actionPerformed(ActionEvent e)
\r
2515 int s, sSize = viewport.alignment.getHeight();
\r
2516 SequenceI [] newSeq = new SequenceI[sSize];
\r
2519 StringBuffer protein;
\r
2521 for(s=0; s<sSize; s++)
\r
2523 protein = new StringBuffer();
\r
2524 seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
\r
2525 resSize = seq.length();
\r
2526 for(res = 0; res < resSize; res+=3)
\r
2528 String codon = seq.substring(res, res+3);
\r
2529 codon = codon.replace('U', 'T');
\r
2530 String aa = ResidueProperties.codonTranslate(codon);
\r
2532 protein.append(viewport.getGapCharacter());
\r
2533 else if(aa.equals("STOP"))
\r
2534 protein.append("X");
\r
2536 protein.append( aa );
\r
2538 newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
\r
2542 AlignmentI al = new Alignment(newSeq);
\r
2543 al.setDataset(null);
\r
2546 ////////////////////////////////
\r
2547 // Copy annotations across
\r
2548 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2549 = viewport.alignment.getAlignmentAnnotation();
\r
2551 for (int i = 0; i < annotations.length; i++)
\r
2554 if (annotations[i].label.equals("Quality") ||
\r
2555 annotations[i].label.equals("Conservation") ||
\r
2556 annotations[i].label.equals("Consensus"))
\r
2562 aSize = viewport.alignment.getWidth()/3;
\r
2563 jalview.datamodel.Annotation [] anots =
\r
2564 new jalview.datamodel.Annotation[aSize];
\r
2566 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2568 if( annotations[i].annotations[a]==null
\r
2569 || annotations[i].annotations[a]==null)
\r
2572 anots[a/3] = new Annotation(
\r
2573 annotations[i].annotations[a].displayCharacter,
\r
2574 annotations[i].annotations[a].description,
\r
2575 annotations[i].annotations[a].secondaryStructure,
\r
2576 annotations[i].annotations[a].value,
\r
2577 annotations[i].annotations[a].colour);
\r
2580 jalview.datamodel.AlignmentAnnotation aa
\r
2581 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2582 annotations[i].description, anots );
\r
2583 al.addAnnotation(aa);
\r
2587 AlignFrame af = new AlignFrame(al);
\r
2588 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2590 NEW_WINDOW_HEIGHT);
\r
2593 // AlignViewport newViewport = new AlignViewport(al);
\r
2594 // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2595 // tabbedPane.add("Protein", ap);
\r
2596 // viewports.add(newViewport);
\r
2597 // alignPanels.add(ap);
\r
2600 /////////////////////////
\r
2602 // AlignViewport ds = new AlignViewport(al.getDataset());
\r
2603 // ds.setDataset(true);
\r
2604 // AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2605 // tabbedPane.add("Dataset", dap);
\r
2606 // viewports.add(ds);
\r
2607 // alignPanels.add(dap);
\r
2608 /////////////////////////
\r
2613 /*public void tabSelected()
\r
2615 int index = tabbedPane.getSelectedIndex();
\r
2616 viewport = (AlignViewport)viewports.elementAt(index);
\r
2617 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r