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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30 import javax.swing.event.*;
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32 import jalview.analysis.*;
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33 import jalview.datamodel.*;
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34 import jalview.io.*;
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35 import jalview.jbgui.*;
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36 import jalview.schemes.*;
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37 import jalview.ws.*;
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43 * @version $Revision$
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45 public class AlignFrame
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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 final AlignmentPanel alignPanel;
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54 final AlignViewport viewport;
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56 /** DOCUMENT ME!! */
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57 public String currentFileFormat = null;
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58 Stack historyList = new Stack();
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59 Stack redoList = new Stack();
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60 private int treeCount = 0;
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63 * Creates a new AlignFrame object.
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65 * @param al DOCUMENT ME!
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67 public AlignFrame(AlignmentI al)
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69 viewport = new AlignViewport(al);
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71 if(viewport.vconsensus==null)
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73 //Out of memory caluclating consensus.
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74 BLOSUM62Colour.setEnabled(false);
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75 PIDColour.setEnabled(false);
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76 conservationMenuItem.setEnabled(false);
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77 modifyConservation.setEnabled(false);
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78 abovePIDThreshold.setEnabled(false);
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79 modifyPID.setEnabled(false);
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82 alignPanel = new AlignmentPanel(this, viewport);
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83 alignPanel.annotationPanel.adjustPanelHeight();
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84 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
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85 annotationPanel.getPreferredSize());
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86 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
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87 getPreferredSize());
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88 alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
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90 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
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92 if(sortby.equals("Id"))
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93 sortIDMenuItem_actionPerformed(null);
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94 else if(sortby.equals("Pairwise Identity"))
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95 sortPairwiseMenuItem_actionPerformed(null);
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97 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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99 viewport.addPropertyChangeListener(new PropertyChangeListener()
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101 public void propertyChange(PropertyChangeEvent evt)
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103 if (evt.getPropertyName().equals("alignment"))
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105 alignmentChanged();
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110 if(Desktop.desktop!=null)
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111 addServiceListeners();
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114 /* Set up intrinsic listeners for dynamically generated GUI bits. */
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115 private void addServiceListeners()
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117 final java.beans.PropertyChangeListener thisListener;
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118 // Do this once to get current state
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119 BuildWebServiceMenu();
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120 Desktop.discoverer.addPropertyChangeListener(
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121 thisListener = new java.beans.PropertyChangeListener()
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123 public void propertyChange(PropertyChangeEvent evt)
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125 // System.out.println("Discoverer property change.");
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126 if (evt.getPropertyName().equals("services"))
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128 // System.out.println("Rebuilding web service menu");
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129 BuildWebServiceMenu();
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133 addInternalFrameListener(new javax.swing.event.
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134 InternalFrameAdapter()
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136 public void internalFrameClosed(
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137 javax.swing.event.InternalFrameEvent evt)
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139 // System.out.println("deregistering discoverer listener");
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140 Desktop.discoverer.removePropertyChangeListener(thisListener);
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141 closeMenuItem_actionPerformed(null);
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151 * @param String DOCUMENT ME!
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154 public void parseGroupsFile(String file)
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158 BufferedReader in = new BufferedReader(new FileReader(file));
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159 SequenceI seq = null;
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160 String line, text, token;
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161 UserColourScheme ucs;
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162 int index, start, end;
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163 StringTokenizer st;
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165 while ( (line = in.readLine()) != null)
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167 st = new StringTokenizer(line, "\t");
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168 if (st.countTokens() != 6)
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170 System.out.println("Groups file " + file +
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171 " is invalid. Read help file.");
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175 while (st.hasMoreElements())
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177 text = st.nextToken();
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178 token = st.nextToken();
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179 if (!token.equals("ID_NOT_SPECIFIED"))
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181 index = viewport.alignment.findIndex(viewport.alignment.findName(
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187 index = Integer.parseInt(st.nextToken());
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190 start = Integer.parseInt(st.nextToken());
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191 end = Integer.parseInt(st.nextToken());
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192 ucs = new UserColourScheme(st.nextToken());
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194 seq = viewport.alignment.getSequenceAt(index);
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195 start = seq.findIndex(start) - 1;
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196 end = seq.findIndex(end) - 1;
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198 sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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199 sg.addSequence(seq, true);
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201 viewport.alignment.addGroup(sg);
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206 catch (Exception ex)
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208 System.out.println("Error parsing groups file: " + ex);
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215 * @param e DOCUMENT ME!
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217 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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219 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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224 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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229 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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230 }, currentFileFormat);
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232 chooser.setAcceptAllFileFilterUsed(false);
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233 chooser.setFileView(new JalviewFileView());
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234 chooser.setDialogTitle("Save Alignment to file");
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235 chooser.setToolTipText("Save");
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237 int value = chooser.showSaveDialog(this);
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239 if (value == JalviewFileChooser.APPROVE_OPTION)
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241 currentFileFormat = chooser.getSelectedFormat();
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243 if (currentFileFormat == null)
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245 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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246 "You must select a file format before saving!",
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247 "File format not specified",
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248 JOptionPane.WARNING_MESSAGE);
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249 value = chooser.showSaveDialog(this);
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253 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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254 currentFileFormat);
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256 String choice = chooser.getSelectedFile().getPath();
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257 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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259 saveAlignment(choice, currentFileFormat);
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263 public boolean saveAlignment(String file, String format)
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265 if (format.equalsIgnoreCase("Jalview"))
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267 String shortName = title;
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269 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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271 shortName = shortName.substring(shortName.lastIndexOf(
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272 java.io.File.separatorChar) + 1);
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275 Jalview2XML.SaveAlignment(this, file, shortName);
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277 // USE Jalview2XML to save this file
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282 String output = new FormatAdapter().formatSequences(format,
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283 viewport.getAlignment().
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285 if (output == null)
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292 java.io.PrintWriter out = new java.io.PrintWriter(
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293 new java.io.FileWriter(file));
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299 catch (Exception ex)
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301 ex.printStackTrace();
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310 * @param e DOCUMENT ME!
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312 protected void outputText_actionPerformed(ActionEvent e)
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314 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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315 Desktop.addInternalFrame(cap,
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316 "Alignment output - " + e.getActionCommand(), 600,
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318 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
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319 viewport.getAlignment().
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326 * @param e DOCUMENT ME!
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328 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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330 new HTMLOutput(viewport);
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333 public void createImageMap(File file, String image)
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335 alignPanel.makePNGImageMap(file, image);
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341 * @param e DOCUMENT ME!
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343 public void createPNG(File f)
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345 alignPanel.makePNG(f);
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351 * @param e DOCUMENT ME!
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353 public void createEPS(File f)
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355 alignPanel.makeEPS(f);
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361 * @param e DOCUMENT ME!
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363 public void printMenuItem_actionPerformed(ActionEvent e)
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365 //Putting in a thread avoids Swing painting problems
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366 PrintThread thread = new PrintThread();
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373 * @param e DOCUMENT ME!
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375 public void closeMenuItem_actionPerformed(ActionEvent e)
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379 PaintRefresher.components.remove(viewport.alignment);
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380 this.setClosed(true);
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382 catch (Exception ex)
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390 void updateEditMenuBar()
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392 if (historyList.size() > 0)
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394 undoMenuItem.setEnabled(true);
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396 HistoryItem hi = (HistoryItem) historyList.peek();
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397 undoMenuItem.setText("Undo " + hi.getDescription());
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401 undoMenuItem.setEnabled(false);
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402 undoMenuItem.setText("Undo");
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405 if (redoList.size() > 0)
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407 redoMenuItem.setEnabled(true);
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409 HistoryItem hi = (HistoryItem) redoList.peek();
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410 redoMenuItem.setText("Redo " + hi.getDescription());
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414 redoMenuItem.setEnabled(false);
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415 redoMenuItem.setText("Redo");
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422 * @param hi DOCUMENT ME!
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424 public void addHistoryItem(HistoryItem hi)
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426 historyList.push(hi);
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427 updateEditMenuBar();
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433 * @param e DOCUMENT ME!
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435 protected void undoMenuItem_actionPerformed(ActionEvent e)
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437 HistoryItem hi = (HistoryItem) historyList.pop();
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438 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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439 HistoryItem.HIDE));
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440 restoreHistoryItem(hi);
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441 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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447 * @param e DOCUMENT ME!
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449 protected void redoMenuItem_actionPerformed(ActionEvent e)
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451 HistoryItem hi = (HistoryItem) redoList.pop();
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452 restoreHistoryItem(hi);
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453 updateEditMenuBar();
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454 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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457 // used by undo and redo
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458 void restoreHistoryItem(HistoryItem hi)
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460 if (hi.getType() == HistoryItem.SORT)
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462 for (int i = 0; i < hi.getSequences().size(); i++)
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464 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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471 for (int i = 0; i < hi.getSequences().size(); i++)
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473 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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475 if (restore.getLength() == 0)
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477 restore.setSequence(hi.getHidden().elementAt(i).toString());
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478 viewport.alignment.getSequences().insertElementAt(restore,
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479 hi.getAlignIndex(i));
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483 restore.setSequence(hi.getHidden().elementAt(i).toString());
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487 if (hi.getType() == HistoryItem.PASTE)
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489 for (int i = viewport.alignment.getHeight() - 1;
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490 i > (hi.getSequences().size() - 1); i--)
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492 viewport.alignment.deleteSequence(i);
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497 updateEditMenuBar();
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499 viewport.firePropertyChange("alignment", null,
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500 viewport.getAlignment().getSequences());
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506 * @param up DOCUMENT ME!
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508 public void moveSelectedSequences(boolean up)
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510 SequenceGroup sg = viewport.getSelectionGroup();
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519 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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521 SequenceI seq = viewport.alignment.getSequenceAt(i);
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523 if (!sg.sequences.contains(seq))
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528 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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530 if (sg.sequences.contains(temp))
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535 viewport.alignment.getSequences().setElementAt(temp, i);
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536 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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541 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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543 SequenceI seq = viewport.alignment.getSequenceAt(i);
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545 if (!sg.sequences.contains(seq))
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550 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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552 if (sg.sequences.contains(temp))
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557 viewport.alignment.getSequences().setElementAt(temp, i);
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558 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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562 alignPanel.repaint();
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568 * @param e DOCUMENT ME!
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570 protected void copy_actionPerformed(ActionEvent e)
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572 if (viewport.getSelectionGroup() == null)
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574 System.out.println("null here");
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578 SequenceGroup sg = viewport.getSelectionGroup();
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580 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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582 Hashtable orderedSeqs = new Hashtable();
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583 SequenceI [] seqs = new SequenceI[sg.getSize()];
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585 for (int i = 0; i < sg.getSize(); i++)
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587 SequenceI seq = sg.getSequenceAt(i);
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588 int index = viewport.alignment.findIndex(seq);
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589 orderedSeqs.put(index + "", seq);
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592 int index = 0, startRes, endRes;
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595 for (int i = 0; i < sg.getSize(); i++)
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597 SequenceI seq = null;
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599 while (seq == null)
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601 if (orderedSeqs.containsKey(index + ""))
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603 seq = (SequenceI) orderedSeqs.get(index + "");
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616 //Returns residue following index if gap
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617 startRes = seq.findPosition(sg.getStartRes());
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620 //Need to find the residue preceeding index if gap
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623 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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625 ch = seq.getCharAt(j);
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626 if (!jalview.util.Comparison.isGap( (ch)))
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634 endRes += seq.getStart() - 1;
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637 seqs[i] = new Sequence(seq.getName(),
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638 seq.getSequence(sg.getStartRes(), sg.getEndRes()+1),
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643 c.setContents(new StringSelection(FastaFile.print(seqs)), null);
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649 * @param e DOCUMENT ME!
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651 protected void pasteNew_actionPerformed(ActionEvent e)
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659 * @param e DOCUMENT ME!
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661 protected void pasteThis_actionPerformed(ActionEvent e)
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663 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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664 HistoryItem.PASTE));
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671 * @param newAlignment DOCUMENT ME!
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673 void paste(boolean newAlignment)
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677 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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678 Transferable contents = c.getContents(this);
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680 if (contents == null)
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685 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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687 String format = IdentifyFile.Identify(str, "Paste");
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688 SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format);
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693 AlignFrame af = new AlignFrame(new Alignment(sequences));
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694 String newtitle = new String("Copied sequences");
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696 if (title.startsWith("Copied sequences"))
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702 newtitle = newtitle.concat("- from " + title);
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705 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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706 NEW_WINDOW_HEIGHT);
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711 for (int i = 0; i < sequences.length; i++)
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712 viewport.alignment.addSequence(sequences[i]);
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714 viewport.setEndSeq(viewport.alignment.getHeight());
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715 viewport.alignment.getWidth();
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716 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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719 catch (Exception ex)
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721 // could be anything being pasted in here
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730 * @param e DOCUMENT ME!
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732 protected void cut_actionPerformed(ActionEvent e)
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734 copy_actionPerformed(null);
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735 delete_actionPerformed(null);
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741 * @param e DOCUMENT ME!
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743 protected void delete_actionPerformed(ActionEvent e)
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746 if (viewport.getSelectionGroup() == null)
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751 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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752 HistoryItem.HIDE));
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754 SequenceGroup sg = viewport.getSelectionGroup();
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755 boolean allSequences = false;
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756 if (sg.sequences.size() == viewport.alignment.getHeight())
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758 allSequences = true;
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761 for (int i = 0; i < sg.sequences.size(); i++)
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763 SequenceI seq = sg.getSequenceAt(i);
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764 int index = viewport.getAlignment().findIndex(seq);
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765 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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767 // If the cut affects all sequences, remove highlighted columns
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770 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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771 sg.getEndRes() + 1);
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774 if (seq.getSequence().length() < 1)
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776 viewport.getAlignment().deleteSequence(seq);
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780 viewport.getAlignment().getSequences().setElementAt(seq, index);
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784 viewport.setSelectionGroup(null);
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785 viewport.alignment.deleteGroup(sg);
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787 viewport.firePropertyChange("alignment", null,
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788 viewport.getAlignment().getSequences());
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792 if (viewport.getAlignment().getHeight() < 1)
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796 this.setClosed(true);
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798 catch (Exception ex)
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807 * @param e DOCUMENT ME!
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809 protected void deleteGroups_actionPerformed(ActionEvent e)
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811 viewport.alignment.deleteAllGroups();
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812 viewport.setSelectionGroup(null);
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813 alignPanel.repaint();
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819 * @param e DOCUMENT ME!
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821 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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823 SequenceGroup sg = new SequenceGroup();
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825 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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828 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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831 sg.setEndRes(viewport.alignment.getWidth() - 1);
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832 viewport.setSelectionGroup(sg);
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833 PaintRefresher.Refresh(null, viewport.alignment);
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839 * @param e DOCUMENT ME!
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841 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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843 viewport.setSelectionGroup(null);
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844 viewport.getColumnSelection().clear();
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845 viewport.setSelectionGroup(null);
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846 alignPanel.annotationPanel.activeRes = null;
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847 PaintRefresher.Refresh(null, viewport.alignment);
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853 * @param e DOCUMENT ME!
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855 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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857 SequenceGroup sg = viewport.getSelectionGroup();
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861 selectAllSequenceMenuItem_actionPerformed(null);
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866 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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869 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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872 PaintRefresher.Refresh(null, viewport.alignment);
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878 * @param e DOCUMENT ME!
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880 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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882 ColumnSelection colSel = viewport.getColumnSelection();
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884 if (colSel.size() > 0)
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886 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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887 HistoryItem.HIDE));
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889 int min = colSel.getMin();
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890 viewport.getAlignment().trimLeft(min);
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891 colSel.compensateForEdit(0, min);
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893 if (viewport.getSelectionGroup() != null)
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895 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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898 Vector groups = viewport.alignment.getGroups();
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900 for (int i = 0; i < groups.size(); i++)
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902 SequenceGroup sg = (SequenceGroup) groups.get(i);
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904 if (!sg.adjustForRemoveLeft(min))
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906 viewport.alignment.deleteGroup(sg);
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910 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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917 * @param e DOCUMENT ME!
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919 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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921 ColumnSelection colSel = viewport.getColumnSelection();
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923 if (colSel.size() > 0)
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925 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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926 HistoryItem.HIDE));
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928 int max = colSel.getMax();
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929 viewport.getAlignment().trimRight(max);
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931 if (viewport.getSelectionGroup() != null)
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933 viewport.getSelectionGroup().adjustForRemoveRight(max);
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936 Vector groups = viewport.alignment.getGroups();
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938 for (int i = 0; i < groups.size(); i++)
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940 SequenceGroup sg = (SequenceGroup) groups.get(i);
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942 if (!sg.adjustForRemoveRight(max))
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944 viewport.alignment.deleteGroup(sg);
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948 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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955 * @param e DOCUMENT ME!
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957 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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959 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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960 viewport.alignment, HistoryItem.HIDE));
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962 //This is to maintain viewport position on first residue
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963 //of first sequence
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964 SequenceI seq = viewport.alignment.getSequenceAt(0);
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965 int startRes = seq.findPosition(viewport.startRes);
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967 viewport.getAlignment().removeGaps();
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969 viewport.setStartRes(seq.findIndex(startRes)-1);
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971 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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977 * @param e DOCUMENT ME!
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979 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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981 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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982 HistoryItem.HIDE));
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984 //This is to maintain viewport position on first residue
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985 //of first sequence
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986 SequenceI seq = viewport.alignment.getSequenceAt(0);
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987 int startRes = seq.findPosition(viewport.startRes);
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993 Vector seqs = null;
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996 int end = viewport.alignment.getWidth();
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998 if (viewport.getSelectionGroup() != null
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999 && viewport.getSelectionGroup().sequences != null
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1000 && viewport.getSelectionGroup().sequences.size() > 0)
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1002 seqs = viewport.getSelectionGroup().sequences;
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1003 start = viewport.getSelectionGroup().getStartRes();
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1004 end = viewport.getSelectionGroup().getEndRes()+1;
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1008 seqs = viewport.alignment.getSequences();
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1011 for (int i = 0; i < seqs.size(); i++)
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1013 current = (SequenceI) seqs.elementAt(i);
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1014 jSize = current.getLength();
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1016 // Removing a range is much quicker than removing gaps
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1017 // one by one for long sequences
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1019 int rangeStart=-1, rangeEnd=-1;
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1023 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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1025 if(rangeStart==-1)
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1040 current.deleteChars(rangeStart, rangeEnd);
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1041 j-=rangeEnd-rangeStart;
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1042 jSize-=rangeEnd-rangeStart;
\r
1050 while (j < end && j < jSize);
\r
1053 current.deleteChars(rangeStart, rangeEnd);
\r
1057 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1059 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1062 public void alignmentChanged()
\r
1064 if(viewport.vconsensus!=null)
\r
1066 viewport.updateConsensus();
\r
1067 viewport.updateConservation();
\r
1069 resetAllColourSchemes();
\r
1070 if(alignPanel.overviewPanel!=null)
\r
1071 alignPanel.overviewPanel.updateOverviewImage();
\r
1073 alignPanel.repaint();
\r
1076 void resetAllColourSchemes()
\r
1078 ColourSchemeI cs = viewport.globalColourScheme;
\r
1081 if (cs instanceof ClustalxColourScheme)
\r
1083 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1084 resetClustalX(viewport.alignment.getSequences(),
\r
1085 viewport.alignment.getWidth());
\r
1088 cs.setConsensus(viewport.vconsensus);
\r
1089 if (cs.conservationApplied())
\r
1091 Alignment al = (Alignment) viewport.alignment;
\r
1092 Conservation c = new Conservation("All",
\r
1093 ResidueProperties.propHash, 3,
\r
1094 al.getSequences(), 0,
\r
1095 al.getWidth() - 1);
\r
1097 c.verdict(false, viewport.ConsPercGaps);
\r
1099 cs.setConservation(c);
\r
1103 int s, sSize = viewport.alignment.getGroups().size();
\r
1104 for(s=0; s<sSize; s++)
\r
1106 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1107 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1109 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1111 sg.recalcConservation();
\r
1118 * @param e DOCUMENT ME!
\r
1120 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1122 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1123 HistoryItem.HIDE));
\r
1125 SequenceI current;
\r
1126 int Width = viewport.getAlignment().getWidth();
\r
1128 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1131 current = viewport.getAlignment().getSequenceAt(i);
\r
1133 if (current.getLength() < Width)
\r
1135 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1139 alignmentChanged();
\r
1145 * @param e DOCUMENT ME!
\r
1147 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1149 JInternalFrame frame = new JInternalFrame();
\r
1150 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1151 frame.setContentPane(finder);
\r
1152 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1153 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1159 * @param e DOCUMENT ME!
\r
1161 public void font_actionPerformed(ActionEvent e)
\r
1163 new FontChooser(alignPanel);
\r
1169 * @param e DOCUMENT ME!
\r
1171 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1173 viewport.setShowFullId(fullSeqId.isSelected());
\r
1175 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1176 alignPanel.repaint();
\r
1182 * @param e DOCUMENT ME!
\r
1184 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1186 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1187 alignPanel.repaint();
\r
1193 * @param e DOCUMENT ME!
\r
1195 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1197 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1198 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1199 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1200 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1201 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1202 alignPanel.repaint();
\r
1208 * @param e DOCUMENT ME!
\r
1210 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1212 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1213 alignPanel.repaint();
\r
1219 * @param e DOCUMENT ME!
\r
1221 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1223 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1224 alignPanel.repaint();
\r
1230 * @param e DOCUMENT ME!
\r
1232 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1234 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1235 alignPanel.repaint();
\r
1241 * @param e DOCUMENT ME!
\r
1243 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1245 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1246 alignPanel.repaint();
\r
1252 * @param e DOCUMENT ME!
\r
1254 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1256 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1257 alignPanel.repaint();
\r
1263 * @param e DOCUMENT ME!
\r
1265 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1267 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1268 alignPanel.repaint();
\r
1274 * @param evt DOCUMENT ME!
\r
1276 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1278 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1280 if (viewport.showSequenceFeatures &&
\r
1281 ! ( (Alignment) viewport.alignment).featuresAdded)
\r
1283 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
\r
1286 ( (Alignment) viewport.alignment).featuresAdded = true;
\r
1289 alignPanel.repaint();
\r
1295 * @param e DOCUMENT ME!
\r
1297 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1299 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1300 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1306 * @param e DOCUMENT ME!
\r
1308 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1310 if (alignPanel.overviewPanel != null)
\r
1315 JInternalFrame frame = new JInternalFrame();
\r
1316 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1317 frame.setContentPane(overview);
\r
1318 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1319 frame.getWidth(), frame.getHeight());
\r
1321 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1322 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1324 public void internalFrameClosed(
\r
1325 javax.swing.event.InternalFrameEvent evt)
\r
1327 alignPanel.setOverviewPanel(null);
\r
1332 alignPanel.setOverviewPanel(overview);
\r
1338 * @param e DOCUMENT ME!
\r
1340 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1342 changeColour(null);
\r
1348 * @param e DOCUMENT ME!
\r
1350 public void clustalColour_actionPerformed(ActionEvent e)
\r
1352 changeColour(new ClustalxColourScheme(
\r
1353 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1359 * @param e DOCUMENT ME!
\r
1361 public void zappoColour_actionPerformed(ActionEvent e)
\r
1363 changeColour(new ZappoColourScheme());
\r
1369 * @param e DOCUMENT ME!
\r
1371 public void taylorColour_actionPerformed(ActionEvent e)
\r
1373 changeColour(new TaylorColourScheme());
\r
1379 * @param e DOCUMENT ME!
\r
1381 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1383 changeColour(new HydrophobicColourScheme());
\r
1389 * @param e DOCUMENT ME!
\r
1391 public void helixColour_actionPerformed(ActionEvent e)
\r
1393 changeColour(new HelixColourScheme());
\r
1399 * @param e DOCUMENT ME!
\r
1401 public void strandColour_actionPerformed(ActionEvent e)
\r
1403 changeColour(new StrandColourScheme());
\r
1409 * @param e DOCUMENT ME!
\r
1411 public void turnColour_actionPerformed(ActionEvent e)
\r
1413 changeColour(new TurnColourScheme());
\r
1419 * @param e DOCUMENT ME!
\r
1421 public void buriedColour_actionPerformed(ActionEvent e)
\r
1423 changeColour(new BuriedColourScheme());
\r
1429 * @param e DOCUMENT ME!
\r
1431 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1433 changeColour(new NucleotideColourScheme());
\r
1439 * @param e DOCUMENT ME!
\r
1441 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1443 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1449 * @param cs DOCUMENT ME!
\r
1451 void changeColour(ColourSchemeI cs)
\r
1453 int threshold = 0;
\r
1457 if (viewport.getAbovePIDThreshold())
\r
1459 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1462 cs.setThreshold(threshold,
\r
1463 viewport.getIgnoreGapsConsensus());
\r
1465 viewport.setGlobalColourScheme(cs);
\r
1469 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1472 if (viewport.getConservationSelected())
\r
1475 Alignment al = (Alignment) viewport.alignment;
\r
1476 Conservation c = new Conservation("All",
\r
1477 ResidueProperties.propHash, 3,
\r
1478 al.getSequences(), 0,
\r
1479 al.getWidth() - 1);
\r
1482 c.verdict(false, viewport.ConsPercGaps);
\r
1484 cs.setConservation(c);
\r
1486 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1491 cs.setConservation(null);
\r
1494 cs.setConsensus(viewport.vconsensus);
\r
1497 viewport.setGlobalColourScheme(cs);
\r
1499 if (viewport.getColourAppliesToAllGroups())
\r
1501 Vector groups = viewport.alignment.getGroups();
\r
1503 for (int i = 0; i < groups.size(); i++)
\r
1505 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1513 if (cs instanceof ClustalxColourScheme)
\r
1515 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1517 else if (cs instanceof UserColourScheme)
\r
1519 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1525 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1527 catch (Exception ex)
\r
1532 if (viewport.getAbovePIDThreshold()
\r
1533 || cs instanceof PIDColourScheme
\r
1534 || cs instanceof Blosum62ColourScheme)
\r
1536 sg.cs.setThreshold(threshold,
\r
1537 viewport.getIgnoreGapsConsensus());
\r
1539 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1543 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1546 if (viewport.getConservationSelected())
\r
1548 Conservation c = new Conservation("Group",
\r
1549 ResidueProperties.propHash, 3,
\r
1551 viewport.alignment.getWidth() - 1);
\r
1553 c.verdict(false, viewport.ConsPercGaps);
\r
1554 sg.cs.setConservation(c);
\r
1557 sg.cs.setConservation(null);
\r
1561 if (alignPanel.getOverviewPanel() != null)
\r
1563 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1566 alignPanel.repaint();
\r
1572 * @param e DOCUMENT ME!
\r
1574 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1576 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1578 SliderPanel.setPIDSliderSource(alignPanel,
\r
1579 viewport.getGlobalColourScheme(),
\r
1581 SliderPanel.showPIDSlider();
\r
1588 * @param e DOCUMENT ME!
\r
1590 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1592 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1594 SliderPanel.setConservationSlider(alignPanel,
\r
1595 viewport.globalColourScheme,
\r
1597 SliderPanel.showConservationSlider();
\r
1604 * @param e DOCUMENT ME!
\r
1606 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1608 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1610 viewport.setAbovePIDThreshold(false);
\r
1611 abovePIDThreshold.setSelected(false);
\r
1613 changeColour(viewport.getGlobalColourScheme());
\r
1615 modifyConservation_actionPerformed(null);
\r
1621 * @param e DOCUMENT ME!
\r
1623 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1625 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1627 conservationMenuItem.setSelected(false);
\r
1628 viewport.setConservationSelected(false);
\r
1630 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1632 changeColour(viewport.getGlobalColourScheme());
\r
1634 modifyPID_actionPerformed(null);
\r
1640 * @param e DOCUMENT ME!
\r
1642 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1644 if (e.getActionCommand().equals("User Defined..."))
\r
1646 new UserDefinedColours(alignPanel, null);
\r
1650 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1651 getUserColourSchemes().get(e.getActionCommand());
\r
1653 changeColour(udc);
\r
1657 public void updateUserColourMenu()
\r
1660 Component[] menuItems = colourMenu.getMenuComponents();
\r
1661 int i, iSize = menuItems.length;
\r
1662 for (i = 0; i < iSize; i++)
\r
1664 if (menuItems[i].getName() != null &&
\r
1665 menuItems[i].getName().equals("USER_DEFINED"))
\r
1667 colourMenu.remove(menuItems[i]);
\r
1671 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1673 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1674 getUserColourSchemes().keys();
\r
1676 while (userColours.hasMoreElements())
\r
1678 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1679 nextElement().toString());
\r
1680 radioItem.setName("USER_DEFINED");
\r
1681 radioItem.addMouseListener(new MouseAdapter()
\r
1683 public void mousePressed(MouseEvent evt)
\r
1685 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1687 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1689 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1690 "Remove from default list?",
\r
1691 "Remove user defined colour",
\r
1692 JOptionPane.YES_NO_OPTION);
\r
1693 if(option == JOptionPane.YES_OPTION)
\r
1695 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1696 colourMenu.remove(radioItem);
\r
1699 radioItem.addActionListener(new ActionListener()
\r
1701 public void actionPerformed(ActionEvent evt)
\r
1703 userDefinedColour_actionPerformed(evt);
\r
1709 radioItem.addActionListener(new ActionListener()
\r
1711 public void actionPerformed(ActionEvent evt)
\r
1713 userDefinedColour_actionPerformed(evt);
\r
1717 colourMenu.insert(radioItem, 15);
\r
1718 colours.add(radioItem);
\r
1726 * @param e DOCUMENT ME!
\r
1728 public void PIDColour_actionPerformed(ActionEvent e)
\r
1730 changeColour(new PIDColourScheme());
\r
1736 * @param e DOCUMENT ME!
\r
1738 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1740 changeColour(new Blosum62ColourScheme());
\r
1746 * @param e DOCUMENT ME!
\r
1748 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1750 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1751 HistoryItem.SORT));
\r
1752 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1753 viewport.getAlignment().getSequenceAt(0));
\r
1754 alignPanel.repaint();
\r
1760 * @param e DOCUMENT ME!
\r
1762 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1764 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1765 HistoryItem.SORT));
\r
1766 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1767 alignPanel.repaint();
\r
1773 * @param e DOCUMENT ME!
\r
1775 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1777 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1778 HistoryItem.SORT));
\r
1780 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1781 alignPanel.repaint();
\r
1787 * @param e DOCUMENT ME!
\r
1789 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1791 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1792 JInternalFrame frame = new JInternalFrame();
\r
1793 frame.setContentPane(sp);
\r
1794 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1801 * @param e DOCUMENT ME!
\r
1803 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1805 if ( (viewport.getSelectionGroup() == null) ||
\r
1806 (viewport.getSelectionGroup().getSize() < 2))
\r
1808 JOptionPane.showInternalMessageDialog(this,
\r
1809 "You must select at least 2 sequences.",
\r
1810 "Invalid Selection",
\r
1811 JOptionPane.WARNING_MESSAGE);
\r
1815 JInternalFrame frame = new JInternalFrame();
\r
1816 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1817 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1824 * @param e DOCUMENT ME!
\r
1826 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1828 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1829 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1830 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1831 (viewport.getAlignment().getHeight() < 4))
\r
1833 JOptionPane.showInternalMessageDialog(this,
\r
1834 "Principal component analysis must take\n" +
\r
1835 "at least 4 input sequences.",
\r
1836 "Sequence selection insufficient",
\r
1837 JOptionPane.WARNING_MESSAGE);
\r
1842 new PCAPanel(viewport);
\r
1848 * @param e DOCUMENT ME!
\r
1850 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1852 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1858 * @param e DOCUMENT ME!
\r
1860 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1862 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1868 * @param e DOCUMENT ME!
\r
1870 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1872 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1878 * @param e DOCUMENT ME!
\r
1880 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1882 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1888 * @param type DOCUMENT ME!
\r
1889 * @param pwType DOCUMENT ME!
\r
1890 * @param title DOCUMENT ME!
\r
1892 void NewTreePanel(String type, String pwType, String title)
\r
1894 final TreePanel tp;
\r
1896 if ( (viewport.getSelectionGroup() != null) &&
\r
1897 (viewport.getSelectionGroup().getSize() > 3))
\r
1900 SequenceGroup sg = viewport.getSelectionGroup();
\r
1902 /* Decide if the selection is a column region */
\r
1903 while (s < sg.sequences.size())
\r
1905 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1908 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1909 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1910 "Try using the Pad function in the edit menu,\n" +
\r
1911 "or one of the multiple sequence alignment web services.",
\r
1912 "Sequences in selection are not aligned",
\r
1913 JOptionPane.WARNING_MESSAGE);
\r
1919 title = title + " on region";
\r
1920 tp = new TreePanel(viewport,
\r
1921 viewport.getSelectionGroup().sequences, type, pwType,
\r
1922 sg.getStartRes(), sg.getEndRes());
\r
1926 //are the sequences aligned?
\r
1927 if (!viewport.alignment.isAligned())
\r
1929 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1930 "The sequences must be aligned before creating a tree.\n" +
\r
1931 "Try using the Pad function in the edit menu,\n" +
\r
1932 "or one of the multiple sequence alignment web services.",
\r
1933 "Sequences not aligned",
\r
1934 JOptionPane.WARNING_MESSAGE);
\r
1939 tp = new TreePanel(viewport,
\r
1940 viewport.getAlignment().getSequences(), type, pwType,
\r
1942 viewport.alignment.getWidth());
\r
1945 addTreeMenuItem(tp, title);
\r
1946 viewport.setCurrentTree(tp.getTree());
\r
1948 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1954 * @param title DOCUMENT ME!
\r
1955 * @param order DOCUMENT ME!
\r
1957 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1959 final JMenuItem item = new JMenuItem("by " + title);
\r
1961 item.addActionListener(new java.awt.event.ActionListener()
\r
1963 public void actionPerformed(ActionEvent e)
\r
1965 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1966 HistoryItem.SORT));
\r
1968 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1969 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1970 alignPanel.repaint();
\r
1976 * Maintain the Order by->Displayed Tree menu.
\r
1977 * Creates a new menu item for a TreePanel with an appropriate
\r
1978 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
1979 * to remove the menu item when the treePanel is closed, and adjust
\r
1980 * the tree leaf to sequence mapping when the alignment is modified.
\r
1981 * @param treePanel Displayed tree window.
\r
1982 * @param title SortBy menu item title.
\r
1984 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1986 final JMenuItem item = new JMenuItem(title);
\r
1990 if (treeCount == 1)
\r
1992 sort.add(sortByTreeMenu);
\r
1995 sortByTreeMenu.add(item);
\r
1996 item.addActionListener(new java.awt.event.ActionListener()
\r
1998 public void actionPerformed(ActionEvent e)
\r
2000 addHistoryItem(new HistoryItem("Tree Sort",
\r
2001 viewport.alignment, HistoryItem.SORT));
\r
2002 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2003 treePanel.getTree());
\r
2004 alignPanel.repaint();
\r
2008 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2009 InternalFrameAdapter()
\r
2011 public void internalFrameClosed(
\r
2012 javax.swing.event.InternalFrameEvent evt)
\r
2015 sortByTreeMenu.remove(item);
\r
2017 if (treeCount == 0)
\r
2019 sort.remove(sortByTreeMenu);
\r
2027 * Work out whether the whole set of sequences
\r
2028 * or just the selected set will be submitted for multiple alignment.
\r
2031 private SequenceI[] gatherSequencesForAlignment()
\r
2033 // Now, check we have enough sequences
\r
2034 SequenceI[] msa = null;
\r
2036 if ( (viewport.getSelectionGroup() != null) &&
\r
2037 (viewport.getSelectionGroup().getSize() > 1))
\r
2039 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2040 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2042 msa = new SequenceI[sz = seqs.getSize()];
\r
2044 for (int i = 0; i < sz; i++)
\r
2046 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2051 Vector seqs = viewport.getAlignment().getSequences();
\r
2053 if (seqs.size() > 1)
\r
2055 msa = new SequenceI[seqs.size()];
\r
2057 for (int i = 0; i < seqs.size(); i++)
\r
2059 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2067 * Decides what is submitted to a secondary structure prediction service,
\r
2068 * the currently selected sequence, or the currently selected alignment
\r
2069 * (where the first sequence in the set is the one that the prediction
\r
2072 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2074 SequenceI seq = null;
\r
2075 SequenceI[] msa = null;
\r
2077 if ( (viewport.getSelectionGroup() != null) &&
\r
2078 (viewport.getSelectionGroup().getSize() > 0))
\r
2080 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2081 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2083 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2085 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2090 msa = new SequenceI[sz = seqs.getSize()];
\r
2092 for (int i = 0; i < sz; i++)
\r
2094 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2100 Vector seqs = viewport.getAlignment().getSequences();
\r
2102 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2104 seq = (SequenceI) seqs.elementAt(0);
\r
2108 msa = new SequenceI[seqs.size()];
\r
2110 for (int i = 0; i < seqs.size(); i++)
\r
2112 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2124 return new SequenceI[]
\r
2134 * @param e DOCUMENT ME!
\r
2136 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2138 // Pick the tree file
\r
2139 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2141 "LAST_DIRECTORY"));
\r
2142 chooser.setFileView(new JalviewFileView());
\r
2143 chooser.setDialogTitle("Select a newick-like tree file");
\r
2144 chooser.setToolTipText("Load a tree file");
\r
2146 int value = chooser.showOpenDialog(null);
\r
2148 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2150 String choice = chooser.getSelectedFile().getPath();
\r
2151 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2155 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2157 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2159 catch (Exception ex)
\r
2161 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2162 "Problem reading tree file",
\r
2164 JOptionPane.WARNING_MESSAGE);
\r
2165 ex.printStackTrace();
\r
2171 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2173 return ShowNewickTree(nf,title,600,500,4,5);
\r
2178 * @param nf DOCUMENT ME!
\r
2179 * @param title DOCUMENT ME!
\r
2181 * @return DOCUMENT ME!
\r
2183 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2185 TreePanel tp = null;
\r
2191 if (nf.getTree() != null)
\r
2193 tp = new TreePanel(viewport,
\r
2194 viewport.getAlignment().getSequences(), nf,
\r
2201 tp.setLocation(x,y);
\r
2204 Desktop.addInternalFrame(tp, title, w, h);
\r
2205 addTreeMenuItem(tp, title);
\r
2208 catch (Exception ex)
\r
2210 ex.printStackTrace();
\r
2221 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2222 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2223 printJob.setPrintable(alignPanel, pf);
\r
2225 if (printJob.printDialog())
\r
2231 catch (Exception PrintException)
\r
2233 PrintException.printStackTrace();
\r
2240 * Generates menu items and listener event actions for web service clients
\r
2243 public void BuildWebServiceMenu()
\r
2245 if ( (Desktop.discoverer.services != null)
\r
2246 && (Desktop.discoverer.services.size() > 0))
\r
2248 Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
\r
2249 Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
\r
2250 Vector wsmenu = new Vector();
\r
2251 if (msaws != null)
\r
2253 // Add any Multiple Sequence Alignment Services
\r
2254 final JMenu msawsmenu = new JMenu("Alignment");
\r
2255 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2257 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2259 final JMenuItem method = new JMenuItem(sh.getName());
\r
2260 method.addActionListener(new ActionListener()
\r
2262 public void actionPerformed(ActionEvent e)
\r
2264 SequenceI[] msa = gatherSequencesForAlignment();
\r
2265 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2271 msawsmenu.add(method);
\r
2272 // Deal with services that we know accept partial alignments.
\r
2273 if (sh.getName().indexOf("lustal") > -1)
\r
2275 // We know that ClustalWS can accept partial alignments for refinement.
\r
2276 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2277 methodR.addActionListener(new ActionListener()
\r
2279 public void actionPerformed(ActionEvent e)
\r
2281 SequenceI[] msa = gatherSequencesForAlignment();
\r
2282 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2288 msawsmenu.add(methodR);
\r
2292 wsmenu.add(msawsmenu);
\r
2294 if (secstrpr != null)
\r
2296 // Add any secondary structure prediction services
\r
2297 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2298 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2300 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2302 final JMenuItem method = new JMenuItem(sh.getName());
\r
2303 method.addActionListener(new ActionListener()
\r
2305 public void actionPerformed(ActionEvent e)
\r
2307 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2308 if (msa.length == 1)
\r
2310 // Single Sequence prediction
\r
2311 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2316 if (msa.length > 1)
\r
2318 // Single Sequence prediction
\r
2319 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2325 secstrmenu.add(method);
\r
2327 wsmenu.add(secstrmenu);
\r
2329 this.webService.removeAll();
\r
2330 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2332 webService.add( (JMenu) wsmenu.get(i));
\r
2337 this.webService.removeAll();
\r
2338 this.webService.add(this.webServiceNoServices);
\r
2340 // TODO: add in rediscovery function
\r
2341 // TODO: reduce code redundancy.
\r
2342 // TODO: group services by location as well as function.
\r