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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849 viewport.setEndSeq(viewport.alignment.getHeight());
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850 viewport.alignment.getWidth();
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851 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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854 catch (Exception ex)
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856 // could be anything being pasted in here
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865 * @param e DOCUMENT ME!
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867 protected void cut_actionPerformed(ActionEvent e)
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869 copy_actionPerformed(null);
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870 delete_actionPerformed(null);
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876 * @param e DOCUMENT ME!
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878 protected void delete_actionPerformed(ActionEvent e)
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881 if (viewport.getSelectionGroup() == null)
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886 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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887 HistoryItem.HIDE));
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889 SequenceGroup sg = viewport.getSelectionGroup();
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890 boolean allSequences = false;
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891 if (sg.sequences.size() == viewport.alignment.getHeight())
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893 allSequences = true;
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896 for (int i = 0; i < sg.sequences.size(); i++)
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898 SequenceI seq = sg.getSequenceAt(i);
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899 int index = viewport.getAlignment().findIndex(seq);
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900 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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902 // If the cut affects all sequences, remove highlighted columns
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905 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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906 sg.getEndRes() + 1);
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909 if (seq.getSequence().length() < 1)
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911 viewport.getAlignment().deleteSequence(seq);
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915 viewport.getAlignment().getSequences().setElementAt(seq, index);
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919 viewport.setSelectionGroup(null);
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920 viewport.alignment.deleteGroup(sg);
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922 viewport.firePropertyChange("alignment", null,
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923 viewport.getAlignment().getSequences());
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927 if (viewport.getAlignment().getHeight() < 1)
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931 this.setClosed(true);
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933 catch (Exception ex)
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942 * @param e DOCUMENT ME!
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944 protected void deleteGroups_actionPerformed(ActionEvent e)
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946 viewport.alignment.deleteAllGroups();
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947 viewport.setSelectionGroup(null);
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948 alignPanel.repaint();
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954 * @param e DOCUMENT ME!
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956 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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958 SequenceGroup sg = new SequenceGroup();
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960 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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963 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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966 sg.setEndRes(viewport.alignment.getWidth() - 1);
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967 viewport.setSelectionGroup(sg);
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968 PaintRefresher.Refresh(null, viewport.alignment);
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974 * @param e DOCUMENT ME!
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976 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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978 viewport.setSelectionGroup(null);
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979 viewport.getColumnSelection().clear();
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980 viewport.setSelectionGroup(null);
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981 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
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982 alignPanel.annotationPanel.activeRes = null;
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983 PaintRefresher.Refresh(null, viewport.alignment);
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989 * @param e DOCUMENT ME!
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991 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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993 SequenceGroup sg = viewport.getSelectionGroup();
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997 selectAllSequenceMenuItem_actionPerformed(null);
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1002 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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1005 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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1008 PaintRefresher.Refresh(null, viewport.alignment);
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1014 * @param e DOCUMENT ME!
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1016 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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1018 ColumnSelection colSel = viewport.getColumnSelection();
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1020 if (colSel.size() > 0)
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1022 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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1023 HistoryItem.HIDE));
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1025 int min = colSel.getMin();
\r
1026 viewport.getAlignment().trimLeft(min);
\r
1027 colSel.compensateForEdit(0, min);
\r
1029 if (viewport.getSelectionGroup() != null)
\r
1031 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
1034 Vector groups = viewport.alignment.getGroups();
\r
1036 for (int i = 0; i < groups.size(); i++)
\r
1038 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1040 if (!sg.adjustForRemoveLeft(min))
\r
1042 viewport.alignment.deleteGroup(sg);
\r
1046 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1053 * @param e DOCUMENT ME!
\r
1055 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
\r
1057 ColumnSelection colSel = viewport.getColumnSelection();
\r
1059 if (colSel.size() > 0)
\r
1061 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
1062 HistoryItem.HIDE));
\r
1064 int max = colSel.getMax();
\r
1065 viewport.getAlignment().trimRight(max);
\r
1067 if (viewport.getSelectionGroup() != null)
\r
1069 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
1072 Vector groups = viewport.alignment.getGroups();
\r
1074 for (int i = 0; i < groups.size(); i++)
\r
1076 SequenceGroup sg = (SequenceGroup) groups.get(i);
\r
1078 if (!sg.adjustForRemoveRight(max))
\r
1080 viewport.alignment.deleteGroup(sg);
\r
1084 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1091 * @param e DOCUMENT ME!
\r
1093 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
\r
1095 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
1096 viewport.alignment, HistoryItem.HIDE));
\r
1098 //This is to maintain viewport position on first residue
\r
1099 //of first sequence
\r
1100 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1101 int startRes = seq.findPosition(viewport.startRes);
\r
1103 viewport.getAlignment().removeGaps();
\r
1105 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1107 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1113 * @param e DOCUMENT ME!
\r
1115 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
\r
1117 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
1118 HistoryItem.HIDE));
\r
1120 //This is to maintain viewport position on first residue
\r
1121 //of first sequence
\r
1122 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
1123 int startRes = seq.findPosition(viewport.startRes);
\r
1126 SequenceI current;
\r
1129 Vector seqs = null;
\r
1132 int end = viewport.alignment.getWidth();
\r
1134 if (viewport.getSelectionGroup() != null
\r
1135 && viewport.getSelectionGroup().sequences != null
\r
1136 && viewport.getSelectionGroup().sequences.size() > 0)
\r
1138 seqs = viewport.getSelectionGroup().sequences;
\r
1139 start = viewport.getSelectionGroup().getStartRes();
\r
1140 end = viewport.getSelectionGroup().getEndRes()+1;
\r
1144 seqs = viewport.alignment.getSequences();
\r
1147 for (int i = 0; i < seqs.size(); i++)
\r
1149 current = (SequenceI) seqs.elementAt(i);
\r
1150 jSize = current.getLength();
\r
1152 // Removing a range is much quicker than removing gaps
\r
1153 // one by one for long sequences
\r
1155 int rangeStart=-1, rangeEnd=-1;
\r
1159 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
1161 if(rangeStart==-1)
\r
1176 current.deleteChars(rangeStart, rangeEnd);
\r
1177 j-=rangeEnd-rangeStart;
\r
1178 jSize-=rangeEnd-rangeStart;
\r
1186 while (j < end && j < jSize);
\r
1189 current.deleteChars(rangeStart, rangeEnd);
\r
1193 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1195 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1198 public void alignmentChanged()
\r
1200 if(viewport.vconsensus!=null)
\r
1202 viewport.updateConsensus();
\r
1203 viewport.updateConservation();
\r
1205 resetAllColourSchemes();
\r
1206 if(alignPanel.overviewPanel!=null)
\r
1207 alignPanel.overviewPanel.updateOverviewImage();
\r
1209 alignPanel.repaint();
\r
1212 void resetAllColourSchemes()
\r
1214 ColourSchemeI cs = viewport.globalColourScheme;
\r
1217 if (cs instanceof ClustalxColourScheme)
\r
1219 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1220 resetClustalX(viewport.alignment.getSequences(),
\r
1221 viewport.alignment.getWidth());
\r
1224 cs.setConsensus(viewport.vconsensus);
\r
1225 if (cs.conservationApplied())
\r
1227 Alignment al = (Alignment) viewport.alignment;
\r
1228 Conservation c = new Conservation("All",
\r
1229 ResidueProperties.propHash, 3,
\r
1230 al.getSequences(), 0,
\r
1231 al.getWidth() - 1);
\r
1233 c.verdict(false, viewport.ConsPercGaps);
\r
1235 cs.setConservation(c);
\r
1239 int s, sSize = viewport.alignment.getGroups().size();
\r
1240 for(s=0; s<sSize; s++)
\r
1242 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1243 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1245 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1247 sg.recalcConservation();
\r
1254 * @param e DOCUMENT ME!
\r
1256 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1258 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1259 HistoryItem.HIDE));
\r
1261 SequenceI current;
\r
1262 int Width = viewport.getAlignment().getWidth();
\r
1264 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1267 current = viewport.getAlignment().getSequenceAt(i);
\r
1269 if (current.getLength() < Width)
\r
1271 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1275 alignmentChanged();
\r
1281 * @param e DOCUMENT ME!
\r
1283 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1285 JInternalFrame frame = new JInternalFrame();
\r
1286 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1287 frame.setContentPane(finder);
\r
1288 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1289 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1295 * @param e DOCUMENT ME!
\r
1297 public void font_actionPerformed(ActionEvent e)
\r
1299 new FontChooser(alignPanel);
\r
1305 * @param e DOCUMENT ME!
\r
1307 protected void seqLimit_actionPerformed(ActionEvent e)
\r
1309 viewport.setShowJVSuffix(seqLimits.isSelected());
\r
1311 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1312 alignPanel.repaint();
\r
1319 * @param e DOCUMENT ME!
\r
1321 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1323 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1324 alignPanel.repaint();
\r
1330 * @param e DOCUMENT ME!
\r
1332 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1334 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1335 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1336 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1337 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1338 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1339 alignPanel.repaint();
\r
1345 * @param e DOCUMENT ME!
\r
1347 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1349 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1350 alignPanel.repaint();
\r
1356 * @param e DOCUMENT ME!
\r
1358 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1360 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1361 alignPanel.repaint();
\r
1367 * @param e DOCUMENT ME!
\r
1369 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1371 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1372 alignPanel.repaint();
\r
1378 * @param e DOCUMENT ME!
\r
1380 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1382 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1383 alignPanel.repaint();
\r
1389 * @param e DOCUMENT ME!
\r
1391 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1393 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1394 alignPanel.repaint();
\r
1400 * @param e DOCUMENT ME!
\r
1402 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1404 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1405 alignPanel.repaint();
\r
1411 * @param evt DOCUMENT ME!
\r
1413 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1415 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1417 if (viewport.showSequenceFeatures)
\r
1419 new SequenceFeatureFetcher(viewport.
\r
1424 featureSettings.setEnabled(true);
\r
1426 alignPanel.repaint();
\r
1432 * @param e DOCUMENT ME!
\r
1434 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1436 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1437 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1443 * @param e DOCUMENT ME!
\r
1445 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1447 if (alignPanel.overviewPanel != null)
\r
1452 JInternalFrame frame = new JInternalFrame();
\r
1453 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1454 frame.setContentPane(overview);
\r
1455 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1456 frame.getWidth(), frame.getHeight());
\r
1458 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1459 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1461 public void internalFrameClosed(
\r
1462 javax.swing.event.InternalFrameEvent evt)
\r
1464 alignPanel.setOverviewPanel(null);
\r
1469 alignPanel.setOverviewPanel(overview);
\r
1475 * @param e DOCUMENT ME!
\r
1477 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1479 changeColour(null);
\r
1485 * @param e DOCUMENT ME!
\r
1487 public void clustalColour_actionPerformed(ActionEvent e)
\r
1489 changeColour(new ClustalxColourScheme(
\r
1490 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1496 * @param e DOCUMENT ME!
\r
1498 public void zappoColour_actionPerformed(ActionEvent e)
\r
1500 changeColour(new ZappoColourScheme());
\r
1506 * @param e DOCUMENT ME!
\r
1508 public void taylorColour_actionPerformed(ActionEvent e)
\r
1510 changeColour(new TaylorColourScheme());
\r
1516 * @param e DOCUMENT ME!
\r
1518 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1520 changeColour(new HydrophobicColourScheme());
\r
1526 * @param e DOCUMENT ME!
\r
1528 public void helixColour_actionPerformed(ActionEvent e)
\r
1530 changeColour(new HelixColourScheme());
\r
1536 * @param e DOCUMENT ME!
\r
1538 public void strandColour_actionPerformed(ActionEvent e)
\r
1540 changeColour(new StrandColourScheme());
\r
1546 * @param e DOCUMENT ME!
\r
1548 public void turnColour_actionPerformed(ActionEvent e)
\r
1550 changeColour(new TurnColourScheme());
\r
1556 * @param e DOCUMENT ME!
\r
1558 public void buriedColour_actionPerformed(ActionEvent e)
\r
1560 changeColour(new BuriedColourScheme());
\r
1566 * @param e DOCUMENT ME!
\r
1568 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1570 changeColour(new NucleotideColourScheme());
\r
1576 * @param e DOCUMENT ME!
\r
1578 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1580 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1586 * @param cs DOCUMENT ME!
\r
1588 void changeColour(ColourSchemeI cs)
\r
1590 int threshold = 0;
\r
1594 if (viewport.getAbovePIDThreshold())
\r
1596 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1599 cs.setThreshold(threshold,
\r
1600 viewport.getIgnoreGapsConsensus());
\r
1602 viewport.setGlobalColourScheme(cs);
\r
1606 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1609 if (viewport.getConservationSelected())
\r
1612 Alignment al = (Alignment) viewport.alignment;
\r
1613 Conservation c = new Conservation("All",
\r
1614 ResidueProperties.propHash, 3,
\r
1615 al.getSequences(), 0,
\r
1616 al.getWidth() - 1);
\r
1619 c.verdict(false, viewport.ConsPercGaps);
\r
1621 cs.setConservation(c);
\r
1623 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1628 cs.setConservation(null);
\r
1631 cs.setConsensus(viewport.vconsensus);
\r
1634 viewport.setGlobalColourScheme(cs);
\r
1636 if (viewport.getColourAppliesToAllGroups())
\r
1638 Vector groups = viewport.alignment.getGroups();
\r
1640 for (int i = 0; i < groups.size(); i++)
\r
1642 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1650 if (cs instanceof ClustalxColourScheme)
\r
1652 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1654 else if (cs instanceof UserColourScheme)
\r
1656 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1662 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1664 catch (Exception ex)
\r
1669 if (viewport.getAbovePIDThreshold()
\r
1670 || cs instanceof PIDColourScheme
\r
1671 || cs instanceof Blosum62ColourScheme)
\r
1673 sg.cs.setThreshold(threshold,
\r
1674 viewport.getIgnoreGapsConsensus());
\r
1676 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1680 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1683 if (viewport.getConservationSelected())
\r
1685 Conservation c = new Conservation("Group",
\r
1686 ResidueProperties.propHash, 3,
\r
1688 viewport.alignment.getWidth() - 1);
\r
1690 c.verdict(false, viewport.ConsPercGaps);
\r
1691 sg.cs.setConservation(c);
\r
1694 sg.cs.setConservation(null);
\r
1698 if (alignPanel.getOverviewPanel() != null)
\r
1700 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1703 alignPanel.repaint();
\r
1709 * @param e DOCUMENT ME!
\r
1711 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1713 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1715 SliderPanel.setPIDSliderSource(alignPanel,
\r
1716 viewport.getGlobalColourScheme(),
\r
1718 SliderPanel.showPIDSlider();
\r
1725 * @param e DOCUMENT ME!
\r
1727 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1729 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1731 SliderPanel.setConservationSlider(alignPanel,
\r
1732 viewport.globalColourScheme,
\r
1734 SliderPanel.showConservationSlider();
\r
1741 * @param e DOCUMENT ME!
\r
1743 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1745 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1747 viewport.setAbovePIDThreshold(false);
\r
1748 abovePIDThreshold.setSelected(false);
\r
1750 changeColour(viewport.getGlobalColourScheme());
\r
1752 modifyConservation_actionPerformed(null);
\r
1758 * @param e DOCUMENT ME!
\r
1760 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1762 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1764 conservationMenuItem.setSelected(false);
\r
1765 viewport.setConservationSelected(false);
\r
1767 changeColour(viewport.getGlobalColourScheme());
\r
1769 modifyPID_actionPerformed(null);
\r
1775 * @param e DOCUMENT ME!
\r
1777 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1779 if (e.getActionCommand().equals("User Defined..."))
\r
1781 new UserDefinedColours(alignPanel, null);
\r
1785 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1786 getUserColourSchemes().get(e.getActionCommand());
\r
1788 changeColour(udc);
\r
1792 public void updateUserColourMenu()
\r
1795 Component[] menuItems = colourMenu.getMenuComponents();
\r
1796 int i, iSize = menuItems.length;
\r
1797 for (i = 0; i < iSize; i++)
\r
1799 if (menuItems[i].getName() != null &&
\r
1800 menuItems[i].getName().equals("USER_DEFINED"))
\r
1802 colourMenu.remove(menuItems[i]);
\r
1806 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1808 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1809 getUserColourSchemes().keys();
\r
1811 while (userColours.hasMoreElements())
\r
1813 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1814 nextElement().toString());
\r
1815 radioItem.setName("USER_DEFINED");
\r
1816 radioItem.addMouseListener(new MouseAdapter()
\r
1818 public void mousePressed(MouseEvent evt)
\r
1820 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1822 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1824 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1825 "Remove from default list?",
\r
1826 "Remove user defined colour",
\r
1827 JOptionPane.YES_NO_OPTION);
\r
1828 if(option == JOptionPane.YES_OPTION)
\r
1830 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1831 colourMenu.remove(radioItem);
\r
1834 radioItem.addActionListener(new ActionListener()
\r
1836 public void actionPerformed(ActionEvent evt)
\r
1838 userDefinedColour_actionPerformed(evt);
\r
1844 radioItem.addActionListener(new ActionListener()
\r
1846 public void actionPerformed(ActionEvent evt)
\r
1848 userDefinedColour_actionPerformed(evt);
\r
1852 colourMenu.insert(radioItem, 15);
\r
1853 colours.add(radioItem);
\r
1861 * @param e DOCUMENT ME!
\r
1863 public void PIDColour_actionPerformed(ActionEvent e)
\r
1865 changeColour(new PIDColourScheme());
\r
1871 * @param e DOCUMENT ME!
\r
1873 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1875 changeColour(new Blosum62ColourScheme());
\r
1881 * @param e DOCUMENT ME!
\r
1883 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1885 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1886 HistoryItem.SORT));
\r
1887 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1888 viewport.getAlignment().getSequenceAt(0));
\r
1889 alignPanel.repaint();
\r
1895 * @param e DOCUMENT ME!
\r
1897 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1899 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1900 HistoryItem.SORT));
\r
1901 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1902 alignPanel.repaint();
\r
1908 * @param e DOCUMENT ME!
\r
1910 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1912 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1913 HistoryItem.SORT));
\r
1915 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1916 alignPanel.repaint();
\r
1922 * @param e DOCUMENT ME!
\r
1924 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1926 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1927 JInternalFrame frame = new JInternalFrame();
\r
1928 frame.setContentPane(sp);
\r
1929 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1936 * @param e DOCUMENT ME!
\r
1938 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1940 if ( (viewport.getSelectionGroup() == null) ||
\r
1941 (viewport.getSelectionGroup().getSize() < 2))
\r
1943 JOptionPane.showInternalMessageDialog(this,
\r
1944 "You must select at least 2 sequences.",
\r
1945 "Invalid Selection",
\r
1946 JOptionPane.WARNING_MESSAGE);
\r
1950 JInternalFrame frame = new JInternalFrame();
\r
1951 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1952 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1959 * @param e DOCUMENT ME!
\r
1961 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1963 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1964 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1965 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1966 (viewport.getAlignment().getHeight() < 4))
\r
1968 JOptionPane.showInternalMessageDialog(this,
\r
1969 "Principal component analysis must take\n" +
\r
1970 "at least 4 input sequences.",
\r
1971 "Sequence selection insufficient",
\r
1972 JOptionPane.WARNING_MESSAGE);
\r
1977 new PCAPanel(viewport);
\r
1983 * @param e DOCUMENT ME!
\r
1985 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1987 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1993 * @param e DOCUMENT ME!
\r
1995 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1997 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
2003 * @param e DOCUMENT ME!
\r
2005 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2007 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
2013 * @param e DOCUMENT ME!
\r
2015 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
2017 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
2023 * @param type DOCUMENT ME!
\r
2024 * @param pwType DOCUMENT ME!
\r
2025 * @param title DOCUMENT ME!
\r
2027 void NewTreePanel(String type, String pwType, String title)
\r
2029 final TreePanel tp;
\r
2031 if ( (viewport.getSelectionGroup() != null) &&
\r
2032 (viewport.getSelectionGroup().getSize() > 3))
\r
2035 SequenceGroup sg = viewport.getSelectionGroup();
\r
2037 /* Decide if the selection is a column region */
\r
2038 while (s < sg.sequences.size())
\r
2040 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
2043 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2044 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
2045 "Try using the Pad function in the edit menu,\n" +
\r
2046 "or one of the multiple sequence alignment web services.",
\r
2047 "Sequences in selection are not aligned",
\r
2048 JOptionPane.WARNING_MESSAGE);
\r
2054 title = title + " on region";
\r
2055 tp = new TreePanel(viewport,
\r
2056 viewport.getSelectionGroup().sequences, type, pwType,
\r
2057 sg.getStartRes(), sg.getEndRes());
\r
2061 //are the sequences aligned?
\r
2062 if (!viewport.alignment.isAligned())
\r
2064 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2065 "The sequences must be aligned before creating a tree.\n" +
\r
2066 "Try using the Pad function in the edit menu,\n" +
\r
2067 "or one of the multiple sequence alignment web services.",
\r
2068 "Sequences not aligned",
\r
2069 JOptionPane.WARNING_MESSAGE);
\r
2074 tp = new TreePanel(viewport,
\r
2075 viewport.getAlignment().getSequences(), type, pwType,
\r
2077 viewport.alignment.getWidth());
\r
2080 addTreeMenuItem(tp, title);
\r
2081 viewport.setCurrentTree(tp.getTree());
\r
2083 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
2089 * @param title DOCUMENT ME!
\r
2090 * @param order DOCUMENT ME!
\r
2092 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
2094 final JMenuItem item = new JMenuItem("by " + title);
\r
2096 item.addActionListener(new java.awt.event.ActionListener()
\r
2098 public void actionPerformed(ActionEvent e)
\r
2100 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
2101 HistoryItem.SORT));
\r
2103 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
2104 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
2105 alignPanel.repaint();
\r
2111 * Maintain the Order by->Displayed Tree menu.
\r
2112 * Creates a new menu item for a TreePanel with an appropriate
\r
2113 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
2114 * to remove the menu item when the treePanel is closed, and adjust
\r
2115 * the tree leaf to sequence mapping when the alignment is modified.
\r
2116 * @param treePanel Displayed tree window.
\r
2117 * @param title SortBy menu item title.
\r
2119 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2121 final JMenuItem item = new JMenuItem(title);
\r
2125 if (treeCount == 1)
\r
2127 sort.add(sortByTreeMenu);
\r
2130 sortByTreeMenu.add(item);
\r
2131 item.addActionListener(new java.awt.event.ActionListener()
\r
2133 public void actionPerformed(ActionEvent e)
\r
2135 addHistoryItem(new HistoryItem("Tree Sort",
\r
2136 viewport.alignment, HistoryItem.SORT));
\r
2137 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2138 treePanel.getTree());
\r
2139 alignPanel.repaint();
\r
2143 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2144 InternalFrameAdapter()
\r
2146 public void internalFrameClosed(
\r
2147 javax.swing.event.InternalFrameEvent evt)
\r
2150 sortByTreeMenu.remove(item);
\r
2152 if (treeCount == 0)
\r
2154 sort.remove(sortByTreeMenu);
\r
2162 * Work out whether the whole set of sequences
\r
2163 * or just the selected set will be submitted for multiple alignment.
\r
2166 private SequenceI[] gatherSequencesForAlignment()
\r
2168 // Now, check we have enough sequences
\r
2169 SequenceI[] msa = null;
\r
2171 if ( (viewport.getSelectionGroup() != null) &&
\r
2172 (viewport.getSelectionGroup().getSize() > 1))
\r
2174 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2175 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2177 msa = new SequenceI[sz = seqs.getSize()];
\r
2179 for (int i = 0; i < sz; i++)
\r
2181 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2186 Vector seqs = viewport.getAlignment().getSequences();
\r
2188 if (seqs.size() > 1)
\r
2190 msa = new SequenceI[seqs.size()];
\r
2192 for (int i = 0; i < seqs.size(); i++)
\r
2194 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2202 * Decides what is submitted to a secondary structure prediction service,
\r
2203 * the currently selected sequence, or the currently selected alignment
\r
2204 * (where the first sequence in the set is the one that the prediction
\r
2207 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2209 SequenceI seq = null;
\r
2210 SequenceI[] msa = null;
\r
2212 if ( (viewport.getSelectionGroup() != null) &&
\r
2213 (viewport.getSelectionGroup().getSize() > 0))
\r
2215 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2216 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2218 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2220 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2225 msa = new SequenceI[sz = seqs.getSize()];
\r
2227 for (int i = 0; i < sz; i++)
\r
2229 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2235 Vector seqs = viewport.getAlignment().getSequences();
\r
2237 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2239 seq = (SequenceI) seqs.elementAt(0);
\r
2243 msa = new SequenceI[seqs.size()];
\r
2245 for (int i = 0; i < seqs.size(); i++)
\r
2247 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2259 return new SequenceI[]
\r
2269 * @param e DOCUMENT ME!
\r
2271 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2273 // Pick the tree file
\r
2274 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2276 "LAST_DIRECTORY"));
\r
2277 chooser.setFileView(new JalviewFileView());
\r
2278 chooser.setDialogTitle("Select a newick-like tree file");
\r
2279 chooser.setToolTipText("Load a tree file");
\r
2281 int value = chooser.showOpenDialog(null);
\r
2283 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2285 String choice = chooser.getSelectedFile().getPath();
\r
2286 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2290 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2292 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2294 catch (Exception ex)
\r
2296 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2297 "Problem reading tree file",
\r
2299 JOptionPane.WARNING_MESSAGE);
\r
2300 ex.printStackTrace();
\r
2306 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2308 return ShowNewickTree(nf,title,600,500,4,5);
\r
2313 * @param nf DOCUMENT ME!
\r
2314 * @param title DOCUMENT ME!
\r
2316 * @return DOCUMENT ME!
\r
2318 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2320 TreePanel tp = null;
\r
2326 if (nf.getTree() != null)
\r
2328 tp = new TreePanel(viewport,
\r
2329 viewport.getAlignment().getSequences(), nf,
\r
2336 tp.setLocation(x,y);
\r
2339 Desktop.addInternalFrame(tp, title, w, h);
\r
2340 addTreeMenuItem(tp, title);
\r
2343 catch (Exception ex)
\r
2345 ex.printStackTrace();
\r
2356 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2357 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2358 printJob.setPrintable(alignPanel, pf);
\r
2360 if (printJob.printDialog())
\r
2366 catch (Exception PrintException)
\r
2368 PrintException.printStackTrace();
\r
2375 * Generates menu items and listener event actions for web service clients
\r
2378 public void BuildWebServiceMenu()
\r
2380 if ( (Discoverer.services != null)
\r
2381 && (Discoverer.services.size() > 0))
\r
2383 Vector msaws = (Vector) Discoverer.services.get("MsaWS");
\r
2384 Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
\r
2385 Vector wsmenu = new Vector();
\r
2386 if (msaws != null)
\r
2388 // Add any Multiple Sequence Alignment Services
\r
2389 final JMenu msawsmenu = new JMenu("Alignment");
\r
2390 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2392 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2394 final JMenuItem method = new JMenuItem(sh.getName());
\r
2395 method.addActionListener(new ActionListener()
\r
2397 public void actionPerformed(ActionEvent e)
\r
2399 SequenceI[] msa = gatherSequencesForAlignment();
\r
2400 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2401 false, true, viewport.getAlignment().getDataset());
\r
2406 msawsmenu.add(method);
\r
2407 // Deal with services that we know accept partial alignments.
\r
2408 if (sh.getName().indexOf("lustal") > -1)
\r
2410 // We know that ClustalWS can accept partial alignments for refinement.
\r
2411 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2412 methodR.addActionListener(new ActionListener()
\r
2414 public void actionPerformed(ActionEvent e)
\r
2416 SequenceI[] msa = gatherSequencesForAlignment();
\r
2417 new jalview.ws.MsaWSClient(sh, title, msa,
\r
2418 true, true, viewport.getAlignment().getDataset());
\r
2423 msawsmenu.add(methodR);
\r
2427 wsmenu.add(msawsmenu);
\r
2429 if (secstrpr != null)
\r
2431 // Add any secondary structure prediction services
\r
2432 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2433 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2435 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2437 final JMenuItem method = new JMenuItem(sh.getName());
\r
2438 method.addActionListener(new ActionListener()
\r
2440 public void actionPerformed(ActionEvent e)
\r
2442 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2443 if (msa.length == 1)
\r
2445 // Single Sequence prediction
\r
2446 new jalview.ws.JPredClient(sh,title, msa[0]);
\r
2450 if (msa.length > 1)
\r
2452 // Single Sequence prediction
\r
2453 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2459 secstrmenu.add(method);
\r
2461 wsmenu.add(secstrmenu);
\r
2463 this.webService.removeAll();
\r
2464 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2466 webService.add( (JMenu) wsmenu.get(i));
\r
2471 this.webService.removeAll();
\r
2472 this.webService.add(this.webServiceNoServices);
\r
2474 // TODO: add in rediscovery function
\r
2475 // TODO: reduce code redundancy.
\r
2476 // TODO: group services by location as well as function.
\r
2479 /* public void vamsasStore_actionPerformed(ActionEvent e)
\r
2481 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2482 getProperty("LAST_DIRECTORY"));
\r
2484 chooser.setFileView(new JalviewFileView());
\r
2485 chooser.setDialogTitle("Export to Vamsas file");
\r
2486 chooser.setToolTipText("Export");
\r
2488 int value = chooser.showSaveDialog(this);
\r
2490 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2492 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
\r
2493 //vs.store(chooser.getSelectedFile().getAbsolutePath() );
\r
2494 vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
\r
2498 public void featureSettings_actionPerformed(ActionEvent e)
\r
2500 new FeatureSettings(viewport, alignPanel);
\r
2505 public void showTranslation_actionPerformed(ActionEvent e)
\r
2507 int s, sSize = viewport.alignment.getHeight();
\r
2508 SequenceI [] newSeq = new SequenceI[sSize];
\r
2511 StringBuffer protein;
\r
2513 for(s=0; s<sSize; s++)
\r
2515 protein = new StringBuffer();
\r
2516 seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
\r
2517 resSize = seq.length();
\r
2518 for(res = 0; res < resSize; res+=3)
\r
2520 String codon = seq.substring(res, res+3);
\r
2521 codon = codon.replace('U', 'T');
\r
2522 String aa = ResidueProperties.codonTranslate(codon);
\r
2524 protein.append(viewport.getGapCharacter());
\r
2525 else if(aa.equals("STOP"))
\r
2526 protein.append("X");
\r
2528 protein.append( aa );
\r
2530 newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
\r
2534 AlignmentI al = new Alignment(newSeq);
\r
2535 al.setDataset(null);
\r
2538 ////////////////////////////////
\r
2539 // Copy annotations across
\r
2540 jalview.datamodel.AlignmentAnnotation[] annotations
\r
2541 = viewport.alignment.getAlignmentAnnotation();
\r
2543 for (int i = 0; i < annotations.length; i++)
\r
2546 if (annotations[i].label.equals("Quality") ||
\r
2547 annotations[i].label.equals("Conservation") ||
\r
2548 annotations[i].label.equals("Consensus"))
\r
2554 aSize = viewport.alignment.getWidth()/3;
\r
2555 jalview.datamodel.Annotation [] anots =
\r
2556 new jalview.datamodel.Annotation[aSize];
\r
2558 for(a=0; a<viewport.alignment.getWidth(); a++)
\r
2560 if( annotations[i].annotations[a]==null
\r
2561 || annotations[i].annotations[a]==null)
\r
2564 anots[a/3] = new Annotation(
\r
2565 annotations[i].annotations[a].displayCharacter,
\r
2566 annotations[i].annotations[a].description,
\r
2567 annotations[i].annotations[a].secondaryStructure,
\r
2568 annotations[i].annotations[a].value,
\r
2569 annotations[i].annotations[a].colour);
\r
2572 jalview.datamodel.AlignmentAnnotation aa
\r
2573 = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
\r
2574 annotations[i].description, anots );
\r
2575 al.addAnnotation(aa);
\r
2579 AlignFrame af = new AlignFrame(al);
\r
2580 Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
\r
2582 NEW_WINDOW_HEIGHT);
\r
2585 // AlignViewport newViewport = new AlignViewport(al);
\r
2586 // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
\r
2587 // tabbedPane.add("Protein", ap);
\r
2588 // viewports.add(newViewport);
\r
2589 // alignPanels.add(ap);
\r
2592 /////////////////////////
\r
2594 // AlignViewport ds = new AlignViewport(al.getDataset());
\r
2595 // ds.setDataset(true);
\r
2596 // AlignmentPanel dap = new AlignmentPanel(this, ds);
\r
2597 // tabbedPane.add("Dataset", dap);
\r
2598 // viewports.add(ds);
\r
2599 // alignPanels.add(dap);
\r
2600 /////////////////////////
\r
2605 /*public void tabSelected()
\r
2607 int index = tabbedPane.getSelectedIndex();
\r
2608 viewport = (AlignViewport)viewports.elementAt(index);
\r
2609 alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
\r