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.getDatasetSequence().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 Sequence newseq = new Sequence(sequences[i].getName(),
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832 sequences[i].getSequence(), sequences[i].getStart(),
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833 sequences[i].getEnd());
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834 viewport.alignment.addSequence(newseq);
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835 if(sequences[i].getDatasetSequence()==null)
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837 ////////////////////////////
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838 //Datset needs extension;
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839 /////////////////////////////
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840 Sequence ds = new Sequence(sequences[i].getName(),
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841 AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
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842 sequences[i].getStart(),
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843 sequences[i].getEnd());
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844 newseq.setDatasetSequence(ds);
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845 viewport.alignment.getDataset().addSequence(ds);
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848 newseq.setDatasetSequence(sequences[i].getDatasetSequence());
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851 viewport.setEndSeq(viewport.alignment.getHeight());
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852 viewport.alignment.getWidth();
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853 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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856 catch (Exception ex)
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858 // could be anything being pasted in here
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867 * @param e DOCUMENT ME!
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869 protected void cut_actionPerformed(ActionEvent e)
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871 copy_actionPerformed(null);
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872 delete_actionPerformed(null);
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878 * @param e DOCUMENT ME!
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880 protected void delete_actionPerformed(ActionEvent e)
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883 if (viewport.getSelectionGroup() == null)
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888 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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889 HistoryItem.HIDE));
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891 SequenceGroup sg = viewport.getSelectionGroup();
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892 boolean allSequences = false;
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893 if (sg.sequences.size() == viewport.alignment.getHeight())
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895 allSequences = true;
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898 for (int i = 0; i < sg.sequences.size(); i++)
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900 SequenceI seq = sg.getSequenceAt(i);
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901 int index = viewport.getAlignment().findIndex(seq);
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902 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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904 // If the cut affects all sequences, remove highlighted columns
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907 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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908 sg.getEndRes() + 1);
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911 if (seq.getSequence().length() < 1)
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913 viewport.getAlignment().deleteSequence(seq);
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917 viewport.getAlignment().getSequences().setElementAt(seq, index);
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921 viewport.setSelectionGroup(null);
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922 viewport.alignment.deleteGroup(sg);
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924 viewport.firePropertyChange("alignment", null,
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925 viewport.getAlignment().getSequences());
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929 if (viewport.getAlignment().getHeight() < 1)
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933 this.setClosed(true);
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935 catch (Exception ex)
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944 * @param e DOCUMENT ME!
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946 protected void deleteGroups_actionPerformed(ActionEvent e)
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948 viewport.alignment.deleteAllGroups();
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949 viewport.setSelectionGroup(null);
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950 alignPanel.repaint();
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956 * @param e DOCUMENT ME!
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958 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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960 SequenceGroup sg = new SequenceGroup();
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962 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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965 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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968 sg.setEndRes(viewport.alignment.getWidth() - 1);
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969 viewport.setSelectionGroup(sg);
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970 PaintRefresher.Refresh(null, viewport.alignment);
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976 * @param e DOCUMENT ME!
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978 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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980 viewport.setSelectionGroup(null);
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981 viewport.getColumnSelection().clear();
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982 viewport.setSelectionGroup(null);
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983 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
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984 alignPanel.annotationPanel.activeRes = null;
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985 PaintRefresher.Refresh(null, viewport.alignment);
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991 * @param e DOCUMENT ME!
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993 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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995 SequenceGroup sg = viewport.getSelectionGroup();
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999 selectAllSequenceMenuItem_actionPerformed(null);
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1004 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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1007 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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1010 PaintRefresher.Refresh(null, viewport.alignment);
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1016 * @param e DOCUMENT ME!
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1018 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1020 ColumnSelection colSel = viewport.getColumnSelection();
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1022 if (colSel.size() > 0)
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1024 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
1025 HistoryItem.HIDE));
\r
1027 int min = colSel.getMin();
\r
1028 viewport.getAlignment().trimLeft(min);
\r
1029 colSel.compensateForEdit(0, min);
\r
1031 if (viewport.getSelectionGroup() != null)
\r
1033 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1036 Vector groups = viewport.alignment.getGroups();
\r
1038 for (int i = 0; i < groups.size(); i++)
\r
1040 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1042 if (!sg.adjustForRemoveLeft(min))
\r
1044 viewport.alignment.deleteGroup(sg);
\r
1048 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1055 * @param e DOCUMENT ME!
\r
1057 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1059 ColumnSelection colSel = viewport.getColumnSelection();
\r
1061 if (colSel.size() > 0)
\r
1063 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1064 HistoryItem.HIDE));
\r
1066 int max = colSel.getMax();
\r
1067 viewport.getAlignment().trimRight(max);
\r
1069 if (viewport.getSelectionGroup() != null)
\r
1071 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1074 Vector groups = viewport.alignment.getGroups();
\r
1076 for (int i = 0; i < groups.size(); i++)
\r
1078 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1080 if (!sg.adjustForRemoveRight(max))
\r
1082 viewport.alignment.deleteGroup(sg);
\r
1086 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1093 * @param e DOCUMENT ME!
\r
1095 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1097 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1098 viewport.alignment, HistoryItem.HIDE));
\r
1100 //This is to maintain viewport position on first residue
\r
1101 //of first sequence
\r
1102 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1103 int startRes = seq.findPosition(viewport.startRes);
\r
1105 viewport.getAlignment().removeGaps();
\r
1107 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1109 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1115 * @param e DOCUMENT ME!
\r
1117 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1119 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1120 HistoryItem.HIDE));
\r
1122 //This is to maintain viewport position on first residue
\r
1123 //of first sequence
\r
1124 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1125 int startRes = seq.findPosition(viewport.startRes);
\r
1128 SequenceI current;
\r
1131 Vector seqs = null;
\r
1134 int end = viewport.alignment.getWidth();
\r
1136 if (viewport.getSelectionGroup() != null
\r
1137 && viewport.getSelectionGroup().sequences != null
\r
1138 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1140 seqs = viewport.getSelectionGroup().sequences;
\r
1141 start = viewport.getSelectionGroup().getStartRes();
\r
1142 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1146 seqs = viewport.alignment.getSequences();
\r
1149 for (int i = 0; i < seqs.size(); i++)
\r
1151 current = (SequenceI) seqs.elementAt(i);
\r
1152 jSize = current.getLength();
\r
1154 // Removing a range is much quicker than removing gaps
\r
1155 // one by one for long sequences
\r
1157 int rangeStart=-1, rangeEnd=-1;
\r
1161 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1163 if(rangeStart==-1)
\r
1178 current.deleteChars(rangeStart, rangeEnd);
\r
1179 j-=rangeEnd-rangeStart;
\r
1180 jSize-=rangeEnd-rangeStart;
\r
1188 while (j < end && j < jSize);
\r
1191 current.deleteChars(rangeStart, rangeEnd);
\r
1195 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1197 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1200 public void alignmentChanged()
\r
1202 if(viewport.vconsensus!=null)
\r
1204 viewport.updateConsensus();
\r
1205 viewport.updateConservation();
\r
1207 resetAllColourSchemes();
\r
1208 if(alignPanel.overviewPanel!=null)
\r
1209 alignPanel.overviewPanel.updateOverviewImage();
\r
1211 alignPanel.repaint();
\r
1214 void resetAllColourSchemes()
\r
1216 ColourSchemeI cs = viewport.globalColourScheme;
\r
1219 if (cs instanceof ClustalxColourScheme)
\r
1221 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1222 resetClustalX(viewport.alignment.getSequences(),
\r
1223 viewport.alignment.getWidth());
\r
1226 cs.setConsensus(viewport.vconsensus);
\r
1227 if (cs.conservationApplied())
\r
1229 Alignment al = (Alignment) viewport.alignment;
\r
1230 Conservation c = new Conservation("All",
\r
1231 ResidueProperties.propHash, 3,
\r
1232 al.getSequences(), 0,
\r
1233 al.getWidth() - 1);
\r
1235 c.verdict(false, viewport.ConsPercGaps);
\r
1237 cs.setConservation(c);
\r
1241 int s, sSize = viewport.alignment.getGroups().size();
\r
1242 for(s=0; s<sSize; s++)
\r
1244 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1245 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1247 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1249 sg.recalcConservation();
\r
1256 * @param e DOCUMENT ME!
\r
1258 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1260 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1261 HistoryItem.HIDE));
\r
1263 SequenceI current;
\r
1264 int Width = viewport.getAlignment().getWidth();
\r
1266 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1269 current = viewport.getAlignment().getSequenceAt(i);
\r
1271 if (current.getLength() < Width)
\r
1273 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1277 alignmentChanged();
\r
1283 * @param e DOCUMENT ME!
\r
1285 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1287 JInternalFrame frame = new JInternalFrame();
\r
1288 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1289 frame.setContentPane(finder);
\r
1290 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1291 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1297 * @param e DOCUMENT ME!
\r
1299 public void font_actionPerformed(ActionEvent e)
\r
1301 new FontChooser(alignPanel);
\r
1307 * @param e DOCUMENT ME!
\r
1309 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1311 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1313 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1314 alignPanel.repaint();
\r
1321 * @param e DOCUMENT ME!
\r
1323 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1325 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1326 alignPanel.repaint();
\r
1332 * @param e DOCUMENT ME!
\r
1334 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1336 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1337 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1338 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1339 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1340 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1341 alignPanel.repaint();
\r
1347 * @param e DOCUMENT ME!
\r
1349 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1351 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1352 alignPanel.repaint();
\r
1358 * @param e DOCUMENT ME!
\r
1360 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1362 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1363 alignPanel.repaint();
\r
1369 * @param e DOCUMENT ME!
\r
1371 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1373 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1374 alignPanel.repaint();
\r
1380 * @param e DOCUMENT ME!
\r
1382 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1384 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1385 alignPanel.repaint();
\r
1391 * @param e DOCUMENT ME!
\r
1393 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1395 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1396 alignPanel.repaint();
\r
1402 * @param e DOCUMENT ME!
\r
1404 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1406 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1407 alignPanel.repaint();
\r
1413 * @param evt DOCUMENT ME!
\r
1415 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1417 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1419 if (viewport.showSequenceFeatures)
\r
1421 new SequenceFeatureFetcher(viewport.
\r
1426 featureSettings.setEnabled(true);
\r
1428 alignPanel.repaint();
\r
1434 * @param e DOCUMENT ME!
\r
1436 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1438 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1439 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1445 * @param e DOCUMENT ME!
\r
1447 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1449 if (alignPanel.overviewPanel != null)
\r
1454 JInternalFrame frame = new JInternalFrame();
\r
1455 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1456 frame.setContentPane(overview);
\r
1457 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1458 frame.getWidth(), frame.getHeight());
\r
1460 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1461 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1463 public void internalFrameClosed(
\r
1464 javax.swing.event.InternalFrameEvent evt)
\r
1466 alignPanel.setOverviewPanel(null);
\r
1471 alignPanel.setOverviewPanel(overview);
\r
1477 * @param e DOCUMENT ME!
\r
1479 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1481 changeColour(null);
\r
1487 * @param e DOCUMENT ME!
\r
1489 public void clustalColour_actionPerformed(ActionEvent e)
\r
1491 changeColour(new ClustalxColourScheme(
\r
1492 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1498 * @param e DOCUMENT ME!
\r
1500 public void zappoColour_actionPerformed(ActionEvent e)
\r
1502 changeColour(new ZappoColourScheme());
\r
1508 * @param e DOCUMENT ME!
\r
1510 public void taylorColour_actionPerformed(ActionEvent e)
\r
1512 changeColour(new TaylorColourScheme());
\r
1518 * @param e DOCUMENT ME!
\r
1520 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1522 changeColour(new HydrophobicColourScheme());
\r
1528 * @param e DOCUMENT ME!
\r
1530 public void helixColour_actionPerformed(ActionEvent e)
\r
1532 changeColour(new HelixColourScheme());
\r
1538 * @param e DOCUMENT ME!
\r
1540 public void strandColour_actionPerformed(ActionEvent e)
\r
1542 changeColour(new StrandColourScheme());
\r
1548 * @param e DOCUMENT ME!
\r
1550 public void turnColour_actionPerformed(ActionEvent e)
\r
1552 changeColour(new TurnColourScheme());
\r
1558 * @param e DOCUMENT ME!
\r
1560 public void buriedColour_actionPerformed(ActionEvent e)
\r
1562 changeColour(new BuriedColourScheme());
\r
1568 * @param e DOCUMENT ME!
\r
1570 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1572 changeColour(new NucleotideColourScheme());
\r
1578 * @param e DOCUMENT ME!
\r
1580 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1582 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1588 * @param cs DOCUMENT ME!
\r
1590 void changeColour(ColourSchemeI cs)
\r
1592 int threshold = 0;
\r
1596 if (viewport.getAbovePIDThreshold())
\r
1598 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1601 cs.setThreshold(threshold,
\r
1602 viewport.getIgnoreGapsConsensus());
\r
1604 viewport.setGlobalColourScheme(cs);
\r
1608 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1611 if (viewport.getConservationSelected())
\r
1614 Alignment al = (Alignment) viewport.alignment;
\r
1615 Conservation c = new Conservation("All",
\r
1616 ResidueProperties.propHash, 3,
\r
1617 al.getSequences(), 0,
\r
1618 al.getWidth() - 1);
\r
1621 c.verdict(false, viewport.ConsPercGaps);
\r
1623 cs.setConservation(c);
\r
1625 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1630 cs.setConservation(null);
\r
1633 cs.setConsensus(viewport.vconsensus);
\r
1636 viewport.setGlobalColourScheme(cs);
\r
1638 if (viewport.getColourAppliesToAllGroups())
\r
1640 Vector groups = viewport.alignment.getGroups();
\r
1642 for (int i = 0; i < groups.size(); i++)
\r
1644 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1652 if (cs instanceof ClustalxColourScheme)
\r
1654 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1656 else if (cs instanceof UserColourScheme)
\r
1658 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1664 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1666 catch (Exception ex)
\r
1671 if (viewport.getAbovePIDThreshold()
\r
1672 || cs instanceof PIDColourScheme
\r
1673 || cs instanceof Blosum62ColourScheme)
\r
1675 sg.cs.setThreshold(threshold,
\r
1676 viewport.getIgnoreGapsConsensus());
\r
1678 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1682 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1685 if (viewport.getConservationSelected())
\r
1687 Conservation c = new Conservation("Group",
\r
1688 ResidueProperties.propHash, 3,
\r
1690 viewport.alignment.getWidth() - 1);
\r
1692 c.verdict(false, viewport.ConsPercGaps);
\r
1693 sg.cs.setConservation(c);
\r
1696 sg.cs.setConservation(null);
\r
1700 if (alignPanel.getOverviewPanel() != null)
\r
1702 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1705 alignPanel.repaint();
\r
1711 * @param e DOCUMENT ME!
\r
1713 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1715 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1717 SliderPanel.setPIDSliderSource(alignPanel,
\r
1718 viewport.getGlobalColourScheme(),
\r
1720 SliderPanel.showPIDSlider();
\r
1727 * @param e DOCUMENT ME!
\r
1729 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1731 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1733 SliderPanel.setConservationSlider(alignPanel,
\r
1734 viewport.globalColourScheme,
\r
1736 SliderPanel.showConservationSlider();
\r
1743 * @param e DOCUMENT ME!
\r
1745 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1747 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1749 viewport.setAbovePIDThreshold(false);
\r
1750 abovePIDThreshold.setSelected(false);
\r
1752 changeColour(viewport.getGlobalColourScheme());
\r
1754 modifyConservation_actionPerformed(null);
\r
1760 * @param e DOCUMENT ME!
\r
1762 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1764 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1766 conservationMenuItem.setSelected(false);
\r
1767 viewport.setConservationSelected(false);
\r
1769 changeColour(viewport.getGlobalColourScheme());
\r
1771 modifyPID_actionPerformed(null);
\r
1777 * @param e DOCUMENT ME!
\r
1779 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1781 if (e.getActionCommand().equals("User Defined..."))
\r
1783 new UserDefinedColours(alignPanel, null);
\r
1787 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1788 getUserColourSchemes().get(e.getActionCommand());
\r
1790 changeColour(udc);
\r
1794 public void updateUserColourMenu()
\r
1797 Component[] menuItems = colourMenu.getMenuComponents();
\r
1798 int i, iSize = menuItems.length;
\r
1799 for (i = 0; i < iSize; i++)
\r
1801 if (menuItems[i].getName() != null &&
\r
1802 menuItems[i].getName().equals("USER_DEFINED"))
\r
1804 colourMenu.remove(menuItems[i]);
\r
1808 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1810 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1811 getUserColourSchemes().keys();
\r
1813 while (userColours.hasMoreElements())
\r
1815 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1816 nextElement().toString());
\r
1817 radioItem.setName("USER_DEFINED");
\r
1818 radioItem.addMouseListener(new MouseAdapter()
\r
1820 public void mousePressed(MouseEvent evt)
\r
1822 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1824 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1826 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1827 "Remove from default list?",
\r
1828 "Remove user defined colour",
\r
1829 JOptionPane.YES_NO_OPTION);
\r
1830 if(option == JOptionPane.YES_OPTION)
\r
1832 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1833 colourMenu.remove(radioItem);
\r
1836 radioItem.addActionListener(new ActionListener()
\r
1838 public void actionPerformed(ActionEvent evt)
\r
1840 userDefinedColour_actionPerformed(evt);
\r
1846 radioItem.addActionListener(new ActionListener()
\r
1848 public void actionPerformed(ActionEvent evt)
\r
1850 userDefinedColour_actionPerformed(evt);
\r
1854 colourMenu.insert(radioItem, 15);
\r
1855 colours.add(radioItem);
\r
1863 * @param e DOCUMENT ME!
\r
1865 public void PIDColour_actionPerformed(ActionEvent e)
\r
1867 changeColour(new PIDColourScheme());
\r
1873 * @param e DOCUMENT ME!
\r
1875 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1877 changeColour(new Blosum62ColourScheme());
\r
1883 * @param e DOCUMENT ME!
\r
1885 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1887 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1888 HistoryItem.SORT));
\r
1889 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1890 viewport.getAlignment().getSequenceAt(0));
\r
1891 alignPanel.repaint();
\r
1897 * @param e DOCUMENT ME!
\r
1899 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1901 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1902 HistoryItem.SORT));
\r
1903 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1904 alignPanel.repaint();
\r
1910 * @param e DOCUMENT ME!
\r
1912 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1914 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1915 HistoryItem.SORT));
\r
1917 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1918 alignPanel.repaint();
\r
1924 * @param e DOCUMENT ME!
\r
1926 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1928 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1929 JInternalFrame frame = new JInternalFrame();
\r
1930 frame.setContentPane(sp);
\r
1931 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1938 * @param e DOCUMENT ME!
\r
1940 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1942 if ( (viewport.getSelectionGroup() == null) ||
\r
1943 (viewport.getSelectionGroup().getSize() < 2))
\r
1945 JOptionPane.showInternalMessageDialog(this,
\r
1946 "You must select at least 2 sequences.",
\r
1947 "Invalid Selection",
\r
1948 JOptionPane.WARNING_MESSAGE);
\r
1952 JInternalFrame frame = new JInternalFrame();
\r
1953 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1954 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1961 * @param e DOCUMENT ME!
\r
1963 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1965 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1966 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1967 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1968 (viewport.getAlignment().getHeight() < 4))
\r
1970 JOptionPane.showInternalMessageDialog(this,
\r
1971 "Principal component analysis must take\n" +
\r
1972 "at least 4 input sequences.",
\r
1973 "Sequence selection insufficient",
\r
1974 JOptionPane.WARNING_MESSAGE);
\r
1979 new PCAPanel(viewport);
\r
1985 * @param e DOCUMENT ME!
\r
1987 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1989 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1995 * @param e DOCUMENT ME!
\r
1997 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1999 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2005 * @param e DOCUMENT ME!
\r
2007 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2009 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2015 * @param e DOCUMENT ME!
\r
2017 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2019 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2025 * @param type DOCUMENT ME!
\r
2026 * @param pwType DOCUMENT ME!
\r
2027 * @param title DOCUMENT ME!
\r
2029 void NewTreePanel(String type, String pwType, String title)
\r
2031 final TreePanel tp;
\r
2033 if ( (viewport.getSelectionGroup() != null) &&
\r
2034 (viewport.getSelectionGroup().getSize() > 3))
\r
2037 SequenceGroup sg = viewport.getSelectionGroup();
\r
2039 /* Decide if the selection is a column region */
\r
2040 while (s < sg.sequences.size())
\r
2042 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2045 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2046 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2047 "Try using the Pad function in the edit menu,\n" +
\r
2048 "or one of the multiple sequence alignment web services.",
\r
2049 "Sequences in selection are not aligned",
\r
2050 JOptionPane.WARNING_MESSAGE);
\r
2056 title = title + " on region";
\r
2057 tp = new TreePanel(viewport,
\r
2058 viewport.getSelectionGroup().sequences, type, pwType,
\r
2059 sg.getStartRes(), sg.getEndRes());
\r
2063 //are the sequences aligned?
\r
2064 if (!viewport.alignment.isAligned())
\r
2066 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2067 "The sequences must be aligned before creating a tree.\n" +
\r
2068 "Try using the Pad function in the edit menu,\n" +
\r
2069 "or one of the multiple sequence alignment web services.",
\r
2070 "Sequences not aligned",
\r
2071 JOptionPane.WARNING_MESSAGE);
\r
2076 tp = new TreePanel(viewport,
\r
2077 viewport.getAlignment().getSequences(), type, pwType,
\r
2079 viewport.alignment.getWidth());
\r
2082 addTreeMenuItem(tp, title);
\r
2083 viewport.setCurrentTree(tp.getTree());
\r
2085 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2091 * @param title DOCUMENT ME!
\r
2092 * @param order DOCUMENT ME!
\r
2094 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2096 final JMenuItem item = new JMenuItem("by " + title);
\r
2098 item.addActionListener(new java.awt.event.ActionListener()
\r
2100 public void actionPerformed(ActionEvent e)
\r
2102 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2103 HistoryItem.SORT));
\r
2105 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2106 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2107 alignPanel.repaint();
\r
2113 * Maintain the Order by->Displayed Tree menu.
\r
2114 * Creates a new menu item for a TreePanel with an appropriate
\r
2115 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2116 * to remove the menu item when the treePanel is closed, and adjust
\r
2117 * the tree leaf to sequence mapping when the alignment is modified.
\r
2118 * @param treePanel Displayed tree window.
\r
2119 * @param title SortBy menu item title.
\r
2121 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2123 final JMenuItem item = new JMenuItem(title);
\r
2127 if (treeCount == 1)
\r
2129 sort.add(sortByTreeMenu);
\r
2132 sortByTreeMenu.add(item);
\r
2133 item.addActionListener(new java.awt.event.ActionListener()
\r
2135 public void actionPerformed(ActionEvent e)
\r
2137 addHistoryItem(new HistoryItem("Tree Sort",
\r
2138 viewport.alignment, HistoryItem.SORT));
\r
2139 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2140 treePanel.getTree());
\r
2141 alignPanel.repaint();
\r
2145 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2146 InternalFrameAdapter()
\r
2148 public void internalFrameClosed(
\r
2149 javax.swing.event.InternalFrameEvent evt)
\r
2152 sortByTreeMenu.remove(item);
\r
2154 if (treeCount == 0)
\r
2156 sort.remove(sortByTreeMenu);
\r
2164 * Work out whether the whole set of sequences
\r
2165 * or just the selected set will be submitted for multiple alignment.
\r
2168 private SequenceI[] gatherSequencesForAlignment()
\r
2170 // Now, check we have enough sequences
\r
2171 SequenceI[] msa = null;
\r
2173 if ( (viewport.getSelectionGroup() != null) &&
\r
2174 (viewport.getSelectionGroup().getSize() > 1))
\r
2176 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2177 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2179 msa = new SequenceI[sz = seqs.getSize()];
\r
2181 for (int i = 0; i < sz; i++)
\r
2183 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2188 Vector seqs = viewport.getAlignment().getSequences();
\r
2190 if (seqs.size() > 1)
\r
2192 msa = new SequenceI[seqs.size()];
\r
2194 for (int i = 0; i < seqs.size(); i++)
\r
2196 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2204 * Decides what is submitted to a secondary structure prediction service,
\r
2205 * the currently selected sequence, or the currently selected alignment
\r
2206 * (where the first sequence in the set is the one that the prediction
\r
2209 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2211 SequenceI seq = null;
\r
2212 SequenceI[] msa = null;
\r
2214 if ( (viewport.getSelectionGroup() != null) &&
\r
2215 (viewport.getSelectionGroup().getSize() > 0))
\r
2217 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2218 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2220 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2222 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2227 msa = new SequenceI[sz = seqs.getSize()];
\r
2229 for (int i = 0; i < sz; i++)
\r
2231 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2237 Vector seqs = viewport.getAlignment().getSequences();
\r
2239 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2241 seq = (SequenceI) seqs.elementAt(0);
\r
2245 msa = new SequenceI[seqs.size()];
\r
2247 for (int i = 0; i < seqs.size(); i++)
\r
2249 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2261 return new SequenceI[]
\r
2271 * @param e DOCUMENT ME!
\r
2273 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2275 // Pick the tree file
\r
2276 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2278 "LAST_DIRECTORY"));
\r
2279 chooser.setFileView(new JalviewFileView());
\r
2280 chooser.setDialogTitle("Select a newick-like tree file");
\r
2281 chooser.setToolTipText("Load a tree file");
\r
2283 int value = chooser.showOpenDialog(null);
\r
2285 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2287 String choice = chooser.getSelectedFile().getPath();
\r
2288 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2292 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2294 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2296 catch (Exception ex)
\r
2298 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2299 "Problem reading tree file",
\r
2301 JOptionPane.WARNING_MESSAGE);
\r
2302 ex.printStackTrace();
\r
2308 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2310 return ShowNewickTree(nf,title,600,500,4,5);
\r
2315 * @param nf DOCUMENT ME!
\r
2316 * @param title DOCUMENT ME!
\r
2318 * @return DOCUMENT ME!
\r
2320 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2322 TreePanel tp = null;
\r
2328 if (nf.getTree() != null)
\r
2330 tp = new TreePanel(viewport,
\r
2331 viewport.getAlignment().getSequences(), nf,
\r
2338 tp.setLocation(x,y);
\r
2341 Desktop.addInternalFrame(tp, title, w, h);
\r
2342 addTreeMenuItem(tp, title);
\r
2345 catch (Exception ex)
\r
2347 ex.printStackTrace();
\r
2358 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2359 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2360 printJob.setPrintable(alignPanel, pf);
\r
2362 if (printJob.printDialog())
\r
2368 catch (Exception PrintException)
\r
2370 PrintException.printStackTrace();
\r
2377 * Generates menu items and listener event actions for web service clients
\r
2380 public void BuildWebServiceMenu()
\r
2382 if ( (Discoverer.services != null)
\r
2383 && (Discoverer.services.size() > 0))
\r
2385 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2386 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2387 Vector wsmenu = new Vector();
\r
2388 if (msaws != null)
\r
2390 // Add any Multiple Sequence Alignment Services
\r
2391 final JMenu msawsmenu = new JMenu("Alignment");
\r
2392 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2394 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2396 final JMenuItem method = new JMenuItem(sh.getName());
\r
2397 method.addActionListener(new ActionListener()
\r
2399 public void actionPerformed(ActionEvent e)
\r
2401 SequenceI[] msa = gatherSequencesForAlignment();
\r
2402 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2403 false, true, viewport.getAlignment().getDataset());
\r
2408 msawsmenu.add(method);
\r
2409 // Deal with services that we know accept partial alignments.
\r
2410 if (sh.getName().indexOf("lustal") > -1)
\r
2412 // We know that ClustalWS can accept partial alignments for refinement.
\r
2413 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2414 methodR.addActionListener(new ActionListener()
\r
2416 public void actionPerformed(ActionEvent e)
\r
2418 SequenceI[] msa = gatherSequencesForAlignment();
\r
2419 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2420 true, true, viewport.getAlignment().getDataset());
\r
2425 msawsmenu.add(methodR);
\r
2429 wsmenu.add(msawsmenu);
\r
2431 if (secstrpr != null)
\r
2433 // Add any secondary structure prediction services
\r
2434 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2435 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2437 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2439 final JMenuItem method = new JMenuItem(sh.getName());
\r
2440 method.addActionListener(new ActionListener()
\r
2442 public void actionPerformed(ActionEvent e)
\r
2444 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2445 if (msa.length == 1)
\r
2447 // Single Sequence prediction
\r
2448 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2452 if (msa.length > 1)
\r
2454 // Single Sequence prediction
\r
2455 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2461 secstrmenu.add(method);
\r
2463 wsmenu.add(secstrmenu);
\r
2465 this.webService.removeAll();
\r
2466 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2468 webService.add( (JMenu) wsmenu.get(i));
\r
2473 this.webService.removeAll();
\r
2474 this.webService.add(this.webServiceNoServices);
\r
2476 // TODO: add in rediscovery function
\r
2477 // TODO: reduce code redundancy.
\r
2478 // TODO: group services by location as well as function.
\r
2481 /* public void vamsasStore_actionPerformed(ActionEvent e)
\r
2483 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2484 getProperty("LAST_DIRECTORY"));
\r
2486 chooser.setFileView(new JalviewFileView());
\r
2487 chooser.setDialogTitle("Export to Vamsas file");
\r
2488 chooser.setToolTipText("Export");
\r
2490 int value = chooser.showSaveDialog(this);
\r
2492 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2494 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2495 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
2496 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
2500 public void featureSettings_actionPerformed(ActionEvent e)
\r
2502 new FeatureSettings(viewport, alignPanel);
\r
2507 public void showTranslation_actionPerformed(ActionEvent e)
\r
2509 int s, sSize = viewport.alignment.getHeight();
\r
2510 SequenceI [] newSeq = new SequenceI[sSize];
\r
2513 StringBuffer protein;
\r
2515 for(s=0; s<sSize; s++)
\r
2517 protein = new StringBuffer();
\r
2518 seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
\r
2519 resSize = seq.length();
\r
2520 for(res = 0; res < resSize; res+=3)
\r
2522 String codon = seq.substring(res, res+3);
\r
2523 codon = codon.replace('U', 'T');
\r
2524 String aa = ResidueProperties.codonTranslate(codon);
\r
2526 protein.append(viewport.getGapCharacter());
\r
2527 else if(aa.equals("STOP"))
\r
2528 protein.append("X");
\r
2530 protein.append( aa );
\r
2532 newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
\r
2536 AlignmentI al = new Alignment(newSeq);
\r
2537 al.setDataset(null);
\r
2540 ////////////////////////////////
\r
2541 // Copy annotations across
\r
2542 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2543 = viewport.alignment.getAlignmentAnnotation();
\r
2545 for (int i = 0; i < annotations.length; i++)
\r
2548 if (annotations[i].label.equals("Quality") ||
\r
2549 annotations[i].label.equals("Conservation") ||
\r
2550 annotations[i].label.equals("Consensus"))
\r
2556 aSize = viewport.alignment.getWidth()/3;
\r
2557 jalview.datamodel.Annotation [] anots =
\r
2558 new jalview.datamodel.Annotation[aSize];
\r
2560 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2562 if( annotations[i].annotations[a]==null
\r
2563 || annotations[i].annotations[a]==null)
\r
2566 anots[a/3] = new Annotation(
\r
2567 annotations[i].annotations[a].displayCharacter,
\r
2568 annotations[i].annotations[a].description,
\r
2569 annotations[i].annotations[a].secondaryStructure,
\r
2570 annotations[i].annotations[a].value,
\r
2571 annotations[i].annotations[a].colour);
\r
2574 jalview.datamodel.AlignmentAnnotation aa
\r
2575 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2576 annotations[i].description, anots );
\r
2577 al.addAnnotation(aa);
\r
2581 AlignFrame af = new AlignFrame(al);
\r
2582 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2584 NEW_WINDOW_HEIGHT);
\r
2587 // AlignViewport newViewport = new AlignViewport(al);
\r
2588 // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2589 // tabbedPane.add("Protein", ap);
\r
2590 // viewports.add(newViewport);
\r
2591 // alignPanels.add(ap);
\r
2594 /////////////////////////
\r
2596 // AlignViewport ds = new AlignViewport(al.getDataset());
\r
2597 // ds.setDataset(true);
\r
2598 // AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2599 // tabbedPane.add("Dataset", dap);
\r
2600 // viewports.add(ds);
\r
2601 // alignPanels.add(dap);
\r
2602 /////////////////////////
\r
2607 /*public void tabSelected()
\r
2609 int index = tabbedPane.getSelectedIndex();
\r
2610 viewport = (AlignViewport)viewports.elementAt(index);
\r
2611 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r