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 alignPanel = new AlignmentPanel(this, viewport);
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72 alignPanel.annotationPanel.adjustPanelHeight();
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73 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
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74 annotationPanel.getPreferredSize());
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75 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
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76 getPreferredSize());
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77 alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
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79 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
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81 if(sortby.equals("Id"))
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82 sortIDMenuItem_actionPerformed(null);
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83 else if(sortby.equals("Pairwise Identity"))
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84 sortPairwiseMenuItem_actionPerformed(null);
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86 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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88 viewport.addPropertyChangeListener(new PropertyChangeListener()
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90 public void propertyChange(PropertyChangeEvent evt)
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92 if (evt.getPropertyName().equals("alignment"))
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99 addServiceListeners();
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102 /* Set up intrinsic listeners for dynamically generated GUI bits. */
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103 private void addServiceListeners()
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105 final java.beans.PropertyChangeListener thisListener;
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106 // Do this once to get current state
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107 BuildWebServiceMenu();
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108 Desktop.discoverer.addPropertyChangeListener(
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109 thisListener = new java.beans.PropertyChangeListener()
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111 public void propertyChange(PropertyChangeEvent evt)
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113 // System.out.println("Discoverer property change.");
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114 if (evt.getPropertyName().equals("services"))
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116 // System.out.println("Rebuilding web service menu");
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117 BuildWebServiceMenu();
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121 addInternalFrameListener(new javax.swing.event.
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122 InternalFrameAdapter()
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124 public void internalFrameClosed(
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125 javax.swing.event.InternalFrameEvent evt)
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127 // System.out.println("deregistering discoverer listener");
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128 Desktop.discoverer.removePropertyChangeListener(thisListener);
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129 closeMenuItem_actionPerformed(null);
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139 * @param String DOCUMENT ME!
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142 public void parseGroupsFile(String file)
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146 BufferedReader in = new BufferedReader(new FileReader(file));
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147 SequenceI seq = null;
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148 String line, text, token;
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149 UserColourScheme ucs;
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150 int index, start, end;
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151 StringTokenizer st;
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153 while ( (line = in.readLine()) != null)
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155 st = new StringTokenizer(line, "\t");
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156 if (st.countTokens() != 6)
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158 System.out.println("Groups file " + file +
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159 " is invalid. Read help file.");
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163 while (st.hasMoreElements())
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165 text = st.nextToken();
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166 token = st.nextToken();
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167 if (!token.equals("ID_NOT_SPECIFIED"))
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169 index = viewport.alignment.findIndex(viewport.alignment.findName(
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175 index = Integer.parseInt(st.nextToken());
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178 start = Integer.parseInt(st.nextToken());
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179 end = Integer.parseInt(st.nextToken());
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180 ucs = new UserColourScheme(st.nextToken());
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182 seq = viewport.alignment.getSequenceAt(index);
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183 start = seq.findIndex(start) - 1;
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184 end = seq.findIndex(end) - 1;
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186 sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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187 sg.addSequence(seq, true);
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189 viewport.alignment.addGroup(sg);
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194 catch (Exception ex)
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196 System.out.println("Error parsing groups file: " + ex);
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203 * @param e DOCUMENT ME!
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205 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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207 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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212 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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217 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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218 }, currentFileFormat);
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220 chooser.setAcceptAllFileFilterUsed(false);
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221 chooser.setFileView(new JalviewFileView());
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222 chooser.setDialogTitle("Save Alignment to file");
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223 chooser.setToolTipText("Save");
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225 int value = chooser.showSaveDialog(this);
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227 if (value == JalviewFileChooser.APPROVE_OPTION)
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229 currentFileFormat = chooser.getSelectedFormat();
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230 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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231 currentFileFormat);
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233 String choice = chooser.getSelectedFile().getPath();
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234 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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236 saveAlignment(choice, currentFileFormat);
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240 public boolean saveAlignment(String file, String format)
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242 if (format.equalsIgnoreCase("Jalview"))
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244 String shortName = title;
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246 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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248 shortName = shortName.substring(shortName.lastIndexOf(
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249 java.io.File.separatorChar) + 1);
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252 Jalview2XML.SaveAlignment(this, file, shortName);
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254 // USE Jalview2XML to save this file
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259 String output = FormatAdapter.formatSequences(format,
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260 viewport.getAlignment().
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262 if (output == null)
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269 java.io.PrintWriter out = new java.io.PrintWriter(
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270 new java.io.FileWriter(file));
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276 catch (Exception ex)
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278 ex.printStackTrace();
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287 * @param e DOCUMENT ME!
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289 protected void outputText_actionPerformed(ActionEvent e)
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291 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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292 Desktop.addInternalFrame(cap,
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293 "Alignment output - " + e.getActionCommand(), 600,
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295 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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296 viewport.getAlignment().
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303 * @param e DOCUMENT ME!
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305 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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307 new HTMLOutput(viewport);
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310 public void createImageMap(File file, String image)
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312 alignPanel.makePNGImageMap(file, image);
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318 * @param e DOCUMENT ME!
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320 public void createPNG(File f)
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322 alignPanel.makePNG(f);
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328 * @param e DOCUMENT ME!
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330 public void createEPS(File f)
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332 alignPanel.makeEPS(f);
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338 * @param e DOCUMENT ME!
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340 public void printMenuItem_actionPerformed(ActionEvent e)
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342 //Putting in a thread avoids Swing painting problems
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343 PrintThread thread = new PrintThread();
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350 * @param e DOCUMENT ME!
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352 public void closeMenuItem_actionPerformed(ActionEvent e)
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356 PaintRefresher.components.remove(viewport.alignment);
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357 this.setClosed(true);
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359 catch (Exception ex)
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367 void updateEditMenuBar()
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369 if (historyList.size() > 0)
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371 undoMenuItem.setEnabled(true);
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373 HistoryItem hi = (HistoryItem) historyList.peek();
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374 undoMenuItem.setText("Undo " + hi.getDescription());
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378 undoMenuItem.setEnabled(false);
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379 undoMenuItem.setText("Undo");
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382 if (redoList.size() > 0)
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384 redoMenuItem.setEnabled(true);
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386 HistoryItem hi = (HistoryItem) redoList.peek();
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387 redoMenuItem.setText("Redo " + hi.getDescription());
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391 redoMenuItem.setEnabled(false);
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392 redoMenuItem.setText("Redo");
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399 * @param hi DOCUMENT ME!
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401 public void addHistoryItem(HistoryItem hi)
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403 historyList.push(hi);
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404 updateEditMenuBar();
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410 * @param e DOCUMENT ME!
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412 protected void undoMenuItem_actionPerformed(ActionEvent e)
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414 HistoryItem hi = (HistoryItem) historyList.pop();
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415 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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416 HistoryItem.HIDE));
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417 restoreHistoryItem(hi);
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418 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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424 * @param e DOCUMENT ME!
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426 protected void redoMenuItem_actionPerformed(ActionEvent e)
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428 HistoryItem hi = (HistoryItem) redoList.pop();
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429 restoreHistoryItem(hi);
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430 updateEditMenuBar();
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431 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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434 // used by undo and redo
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435 void restoreHistoryItem(HistoryItem hi)
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437 if (hi.getType() == HistoryItem.SORT)
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439 for (int i = 0; i < hi.getSequences().size(); i++)
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441 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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448 for (int i = 0; i < hi.getSequences().size(); i++)
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450 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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452 if (restore.getLength() == 0)
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454 restore.setSequence(hi.getHidden().elementAt(i).toString());
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455 viewport.alignment.getSequences().insertElementAt(restore,
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456 hi.getAlignIndex(i));
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460 restore.setSequence(hi.getHidden().elementAt(i).toString());
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464 if (hi.getType() == HistoryItem.PASTE)
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466 for (int i = viewport.alignment.getHeight() - 1;
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467 i > (hi.getSequences().size() - 1); i--)
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469 viewport.alignment.deleteSequence(i);
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474 updateEditMenuBar();
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476 viewport.firePropertyChange("alignment", null,
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477 viewport.getAlignment().getSequences());
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483 * @param up DOCUMENT ME!
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485 public void moveSelectedSequences(boolean up)
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487 SequenceGroup sg = viewport.getSelectionGroup();
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496 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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498 SequenceI seq = viewport.alignment.getSequenceAt(i);
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500 if (!sg.sequences.contains(seq))
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505 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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507 if (sg.sequences.contains(temp))
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512 viewport.alignment.getSequences().setElementAt(temp, i);
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513 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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518 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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520 SequenceI seq = viewport.alignment.getSequenceAt(i);
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522 if (!sg.sequences.contains(seq))
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527 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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529 if (sg.sequences.contains(temp))
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534 viewport.alignment.getSequences().setElementAt(temp, i);
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535 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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539 alignPanel.repaint();
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545 * @param e DOCUMENT ME!
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547 protected void copy_actionPerformed(ActionEvent e)
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549 if (viewport.getSelectionGroup() == null)
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554 SequenceGroup sg = viewport.getSelectionGroup();
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556 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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557 StringBuffer buffer = new StringBuffer();
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559 Hashtable orderedSeqs = new Hashtable();
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561 for (int i = 0; i < sg.getSize(); i++)
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563 SequenceI seq = sg.getSequenceAt(i);
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564 int index = viewport.alignment.findIndex(seq);
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565 orderedSeqs.put(index + "", seq);
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568 int index = 0, startRes, endRes;
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571 for (int i = 0; i < sg.getSize(); i++)
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573 SequenceI seq = null;
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575 while (seq == null)
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577 if (orderedSeqs.containsKey(index + ""))
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579 seq = (SequenceI) orderedSeqs.get(index + "");
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590 //Returns residue following index if gap
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591 startRes = seq.findPosition(sg.getStartRes());
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594 //Need to find the residue preceeding index if gap
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597 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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599 ch = seq.getCharAt(j);
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600 if (!jalview.util.Comparison.isGap( (ch)))
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608 endRes += seq.getStart() - 1;
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611 buffer.append(seq.getName() + "\t" +
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614 seq.getSequence(sg.getStartRes(),
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615 sg.getEndRes() + 1) + "\n");
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618 c.setContents(new StringSelection(buffer.toString()), null);
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624 * @param e DOCUMENT ME!
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626 protected void pasteNew_actionPerformed(ActionEvent e)
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634 * @param e DOCUMENT ME!
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636 protected void pasteThis_actionPerformed(ActionEvent e)
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638 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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639 HistoryItem.PASTE));
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646 * @param newAlignment DOCUMENT ME!
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648 void paste(boolean newAlignment)
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652 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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653 Transferable contents = c.getContents(this);
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655 if (contents == null)
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660 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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661 StringTokenizer st = new StringTokenizer(str);
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662 ArrayList seqs = new ArrayList();
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664 while (st.hasMoreElements())
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666 String name = st.nextToken();
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667 int start = Integer.parseInt(st.nextToken());
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668 int end = Integer.parseInt(st.nextToken());
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669 Sequence sequence = new Sequence(name, st.nextToken(), start,
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674 viewport.alignment.addSequence(sequence);
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678 seqs.add(sequence);
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684 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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685 seqs.toArray(newSeqs);
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687 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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688 String newtitle = new String("Copied sequences");
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690 if (title.startsWith("Copied sequences"))
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696 newtitle = newtitle.concat("- from " + title);
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699 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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700 NEW_WINDOW_HEIGHT);
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704 viewport.setEndSeq(viewport.alignment.getHeight());
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705 viewport.alignment.getWidth();
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706 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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709 catch (Exception ex)
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711 // could be anything being pasted in here
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720 * @param e DOCUMENT ME!
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722 protected void cut_actionPerformed(ActionEvent e)
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724 copy_actionPerformed(null);
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725 delete_actionPerformed(null);
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731 * @param e DOCUMENT ME!
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733 protected void delete_actionPerformed(ActionEvent e)
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735 boolean seqsdeleted = false;
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737 if (viewport.getSelectionGroup() == null)
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742 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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743 HistoryItem.HIDE));
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745 SequenceGroup sg = viewport.getSelectionGroup();
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746 boolean allSequences = false;
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747 if (sg.sequences.size() == viewport.alignment.getHeight())
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749 allSequences = true;
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752 for (int i = 0; i < sg.sequences.size(); i++)
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754 SequenceI seq = sg.getSequenceAt(i);
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755 int index = viewport.getAlignment().findIndex(seq);
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756 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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758 // If the cut affects all sequences, remove highlighted columns
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761 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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762 sg.getEndRes() + 1);
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765 if (seq.getSequence().length() < 1)
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767 seqsdeleted = true;
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768 viewport.getAlignment().deleteSequence(seq);
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772 viewport.getAlignment().getSequences().setElementAt(seq, index);
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776 viewport.setSelectionGroup(null);
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777 viewport.alignment.deleteGroup(sg);
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779 viewport.firePropertyChange("alignment", null,
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780 viewport.getAlignment().getSequences());
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784 if (viewport.getAlignment().getHeight() < 1)
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788 this.setClosed(true);
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790 catch (Exception ex)
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799 * @param e DOCUMENT ME!
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801 protected void deleteGroups_actionPerformed(ActionEvent e)
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803 viewport.alignment.deleteAllGroups();
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804 viewport.setSelectionGroup(null);
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805 alignPanel.repaint();
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811 * @param e DOCUMENT ME!
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813 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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815 SequenceGroup sg = new SequenceGroup();
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817 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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820 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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823 sg.setEndRes(viewport.alignment.getWidth() - 1);
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824 viewport.setSelectionGroup(sg);
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825 PaintRefresher.Refresh(null, viewport.alignment);
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831 * @param e DOCUMENT ME!
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833 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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835 viewport.setSelectionGroup(null);
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836 viewport.getColumnSelection().clear();
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837 viewport.setSelectionGroup(null);
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838 alignPanel.annotationPanel.activeRes = null;
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839 PaintRefresher.Refresh(null, viewport.alignment);
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845 * @param e DOCUMENT ME!
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847 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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849 SequenceGroup sg = viewport.getSelectionGroup();
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853 selectAllSequenceMenuItem_actionPerformed(null);
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858 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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861 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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864 PaintRefresher.Refresh(null, viewport.alignment);
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870 * @param e DOCUMENT ME!
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872 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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874 ColumnSelection colSel = viewport.getColumnSelection();
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876 if (colSel.size() > 0)
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878 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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879 HistoryItem.HIDE));
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881 int min = colSel.getMin();
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882 viewport.getAlignment().trimLeft(min);
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883 colSel.compensateForEdit(0, min);
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885 if (viewport.getSelectionGroup() != null)
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887 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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890 Vector groups = viewport.alignment.getGroups();
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892 for (int i = 0; i < groups.size(); i++)
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894 SequenceGroup sg = (SequenceGroup) groups.get(i);
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896 if (!sg.adjustForRemoveLeft(min))
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898 viewport.alignment.deleteGroup(sg);
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902 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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909 * @param e DOCUMENT ME!
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911 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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913 ColumnSelection colSel = viewport.getColumnSelection();
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915 if (colSel.size() > 0)
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917 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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918 HistoryItem.HIDE));
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920 int max = colSel.getMax();
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921 viewport.getAlignment().trimRight(max);
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923 if (viewport.getSelectionGroup() != null)
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925 viewport.getSelectionGroup().adjustForRemoveRight(max);
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928 Vector groups = viewport.alignment.getGroups();
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930 for (int i = 0; i < groups.size(); i++)
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932 SequenceGroup sg = (SequenceGroup) groups.get(i);
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934 if (!sg.adjustForRemoveRight(max))
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936 viewport.alignment.deleteGroup(sg);
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940 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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947 * @param e DOCUMENT ME!
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949 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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951 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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952 viewport.alignment, HistoryItem.HIDE));
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954 //This is to maintain viewport position on first residue
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955 //of first sequence
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956 SequenceI seq = viewport.alignment.getSequenceAt(0);
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957 int startRes = seq.findPosition(viewport.startRes);
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959 viewport.getAlignment().removeGaps();
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961 viewport.setStartRes(seq.findIndex(startRes)-1);
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963 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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969 * @param e DOCUMENT ME!
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971 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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973 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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974 HistoryItem.HIDE));
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976 //This is to maintain viewport position on first residue
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977 //of first sequence
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978 SequenceI seq = viewport.alignment.getSequenceAt(0);
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979 int startRes = seq.findPosition(viewport.startRes);
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985 Vector seqs = null;
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988 int end = viewport.alignment.getWidth();
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990 if (viewport.getSelectionGroup() != null
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991 && viewport.getSelectionGroup().sequences != null
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992 && viewport.getSelectionGroup().sequences.size() > 0)
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994 seqs = viewport.getSelectionGroup().sequences;
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995 start = viewport.getSelectionGroup().getStartRes();
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996 end = viewport.getSelectionGroup().getEndRes();
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1000 seqs = viewport.alignment.getSequences();
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1003 for (int i = 0; i < seqs.size(); i++)
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1005 current = (SequenceI) seqs.elementAt(i);
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1006 jSize = current.getLength();
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1012 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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1014 current.deleteCharAt(j);
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1020 while (j < end && j < jSize);
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1023 viewport.setStartRes(seq.findIndex(startRes)-1);
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1026 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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1029 public void alignmentChanged()
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1031 viewport.updateConsensus();
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1032 viewport.updateConservation();
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1033 resetAllColourSchemes();
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1034 alignPanel.repaint();
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1037 void resetAllColourSchemes()
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1039 ColourSchemeI cs = viewport.globalColourScheme;
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1042 if (cs instanceof ClustalxColourScheme)
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1044 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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1045 resetClustalX(viewport.alignment.getSequences(),
\r
1046 viewport.alignment.getWidth());
\r
1049 cs.setConsensus(viewport.vconsensus);
\r
1050 if (cs.conservationApplied())
\r
1052 Alignment al = (Alignment) viewport.alignment;
\r
1053 Conservation c = new Conservation("All",
\r
1054 ResidueProperties.propHash, 3,
\r
1055 al.getSequences(), 0,
\r
1056 al.getWidth() - 1);
\r
1058 c.verdict(false, viewport.ConsPercGaps);
\r
1060 cs.setConservation(c);
\r
1064 int s, sSize = viewport.alignment.getGroups().size();
\r
1065 for(s=0; s<sSize; s++)
\r
1067 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1068 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1070 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1072 sg.recalcConservation();
\r
1079 * @param e DOCUMENT ME!
\r
1081 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1083 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1084 HistoryItem.HIDE));
\r
1086 SequenceI current;
\r
1087 int Width = viewport.getAlignment().getWidth();
\r
1089 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1092 current = viewport.getAlignment().getSequenceAt(i);
\r
1094 if (current.getLength() < Width)
\r
1096 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1100 alignmentChanged();
\r
1106 * @param e DOCUMENT ME!
\r
1108 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1110 JInternalFrame frame = new JInternalFrame();
\r
1111 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1112 frame.setContentPane(finder);
\r
1113 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1114 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1120 * @param e DOCUMENT ME!
\r
1122 public void font_actionPerformed(ActionEvent e)
\r
1124 FontChooser fc = new FontChooser(alignPanel);
\r
1130 * @param e DOCUMENT ME!
\r
1132 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1134 viewport.setShowFullId(fullSeqId.isSelected());
\r
1136 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1137 alignPanel.repaint();
\r
1143 * @param e DOCUMENT ME!
\r
1145 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1147 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1148 alignPanel.repaint();
\r
1154 * @param e DOCUMENT ME!
\r
1156 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1158 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1159 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1160 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1161 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1162 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1163 alignPanel.repaint();
\r
1169 * @param e DOCUMENT ME!
\r
1171 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1173 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1174 alignPanel.repaint();
\r
1180 * @param e DOCUMENT ME!
\r
1182 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1184 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1185 alignPanel.repaint();
\r
1191 * @param e DOCUMENT ME!
\r
1193 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1195 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1196 alignPanel.repaint();
\r
1202 * @param e DOCUMENT ME!
\r
1204 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1206 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1207 alignPanel.repaint();
\r
1213 * @param e DOCUMENT ME!
\r
1215 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1217 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1218 alignPanel.repaint();
\r
1224 * @param e DOCUMENT ME!
\r
1226 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1228 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1229 alignPanel.repaint();
\r
1235 * @param evt DOCUMENT ME!
\r
1237 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1239 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1241 if (viewport.showSequenceFeatures &&
\r
1242 ! ( (Alignment) viewport.alignment).featuresAdded)
\r
1244 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
\r
1247 ( (Alignment) viewport.alignment).featuresAdded = true;
\r
1250 alignPanel.repaint();
\r
1256 * @param e DOCUMENT ME!
\r
1258 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1260 if (annotationPanelMenuItem.isSelected() &&
\r
1261 viewport.getWrapAlignment())
\r
1263 annotationPanelMenuItem.setSelected(false);
\r
1268 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1269 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1275 * @param e DOCUMENT ME!
\r
1277 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1279 if (alignPanel.overviewPanel != null)
\r
1284 JInternalFrame frame = new JInternalFrame();
\r
1285 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1286 frame.setContentPane(overview);
\r
1287 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1288 frame.getWidth(), frame.getHeight());
\r
1290 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1291 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1293 public void internalFrameClosed(
\r
1294 javax.swing.event.InternalFrameEvent evt)
\r
1296 alignPanel.setOverviewPanel(null);
\r
1301 alignPanel.setOverviewPanel(overview);
\r
1307 * @param e DOCUMENT ME!
\r
1309 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1311 changeColour(null);
\r
1317 * @param e DOCUMENT ME!
\r
1319 public void clustalColour_actionPerformed(ActionEvent e)
\r
1321 changeColour(new ClustalxColourScheme(
\r
1322 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1328 * @param e DOCUMENT ME!
\r
1330 public void zappoColour_actionPerformed(ActionEvent e)
\r
1332 changeColour(new ZappoColourScheme());
\r
1338 * @param e DOCUMENT ME!
\r
1340 public void taylorColour_actionPerformed(ActionEvent e)
\r
1342 changeColour(new TaylorColourScheme());
\r
1348 * @param e DOCUMENT ME!
\r
1350 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1352 changeColour(new HydrophobicColourScheme());
\r
1358 * @param e DOCUMENT ME!
\r
1360 public void helixColour_actionPerformed(ActionEvent e)
\r
1362 changeColour(new HelixColourScheme());
\r
1368 * @param e DOCUMENT ME!
\r
1370 public void strandColour_actionPerformed(ActionEvent e)
\r
1372 changeColour(new StrandColourScheme());
\r
1378 * @param e DOCUMENT ME!
\r
1380 public void turnColour_actionPerformed(ActionEvent e)
\r
1382 changeColour(new TurnColourScheme());
\r
1388 * @param e DOCUMENT ME!
\r
1390 public void buriedColour_actionPerformed(ActionEvent e)
\r
1392 changeColour(new BuriedColourScheme());
\r
1398 * @param e DOCUMENT ME!
\r
1400 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1402 changeColour(new NucleotideColourScheme());
\r
1408 * @param e DOCUMENT ME!
\r
1410 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1412 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1418 * @param cs DOCUMENT ME!
\r
1420 void changeColour(ColourSchemeI cs)
\r
1422 int threshold = 0;
\r
1426 if (viewport.getAbovePIDThreshold())
\r
1428 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1431 cs.setThreshold(threshold,
\r
1432 viewport.getIgnoreGapsConsensus());
\r
1434 viewport.setGlobalColourScheme(cs);
\r
1438 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1441 if (viewport.getConservationSelected())
\r
1444 Alignment al = (Alignment) viewport.alignment;
\r
1445 Conservation c = new Conservation("All",
\r
1446 ResidueProperties.propHash, 3,
\r
1447 al.getSequences(), 0,
\r
1448 al.getWidth() - 1);
\r
1451 c.verdict(false, viewport.ConsPercGaps);
\r
1453 cs.setConservation(c);
\r
1455 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1460 cs.setConservation(null);
\r
1463 cs.setConsensus(viewport.vconsensus);
\r
1466 viewport.setGlobalColourScheme(cs);
\r
1468 if (viewport.getColourAppliesToAllGroups())
\r
1470 Vector groups = viewport.alignment.getGroups();
\r
1472 for (int i = 0; i < groups.size(); i++)
\r
1474 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1482 if (cs instanceof ClustalxColourScheme)
\r
1484 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1486 else if (cs instanceof UserColourScheme)
\r
1488 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1494 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1496 catch (Exception ex)
\r
1501 if (viewport.getAbovePIDThreshold()
\r
1502 || cs instanceof PIDColourScheme
\r
1503 || cs instanceof Blosum62ColourScheme)
\r
1505 sg.cs.setThreshold(threshold,
\r
1506 viewport.getIgnoreGapsConsensus());
\r
1508 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1512 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1515 if (viewport.getConservationSelected())
\r
1517 Conservation c = new Conservation("Group",
\r
1518 ResidueProperties.propHash, 3,
\r
1520 viewport.alignment.getWidth() - 1);
\r
1522 c.verdict(false, viewport.ConsPercGaps);
\r
1523 sg.cs.setConservation(c);
\r
1526 sg.cs.setConservation(null);
\r
1530 if (alignPanel.getOverviewPanel() != null)
\r
1532 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1535 alignPanel.repaint();
\r
1541 * @param e DOCUMENT ME!
\r
1543 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1545 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1547 SliderPanel.setPIDSliderSource(alignPanel,
\r
1548 viewport.getGlobalColourScheme(),
\r
1550 SliderPanel.showPIDSlider();
\r
1557 * @param e DOCUMENT ME!
\r
1559 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1561 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1563 SliderPanel.setConservationSlider(alignPanel,
\r
1564 viewport.globalColourScheme,
\r
1566 SliderPanel.showConservationSlider();
\r
1573 * @param e DOCUMENT ME!
\r
1575 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1577 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1579 viewport.setAbovePIDThreshold(false);
\r
1580 abovePIDThreshold.setSelected(false);
\r
1582 changeColour(viewport.getGlobalColourScheme());
\r
1584 modifyConservation_actionPerformed(null);
\r
1590 * @param e DOCUMENT ME!
\r
1592 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1594 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1596 conservationMenuItem.setSelected(false);
\r
1597 viewport.setConservationSelected(false);
\r
1599 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1601 changeColour(viewport.getGlobalColourScheme());
\r
1603 modifyPID_actionPerformed(null);
\r
1609 * @param e DOCUMENT ME!
\r
1611 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1613 if (e.getActionCommand().equals("User Defined..."))
\r
1615 new UserDefinedColours(alignPanel, null);
\r
1619 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1620 getUserColourSchemes().get(e.getActionCommand());
\r
1622 changeColour(udc);
\r
1626 public void updateUserColourMenu()
\r
1629 Component[] menuItems = colourMenu.getMenuComponents();
\r
1630 int i, iSize = menuItems.length;
\r
1631 for (i = 0; i < iSize; i++)
\r
1633 if (menuItems[i].getName() != null &&
\r
1634 menuItems[i].getName().equals("USER_DEFINED"))
\r
1636 colourMenu.remove(menuItems[i]);
\r
1640 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1642 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1643 getUserColourSchemes().keys();
\r
1645 while (userColours.hasMoreElements())
\r
1647 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1648 nextElement().toString());
\r
1649 radioItem.setName("USER_DEFINED");
\r
1650 radioItem.addMouseListener(new MouseAdapter()
\r
1652 public void mousePressed(MouseEvent evt)
\r
1654 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1656 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1658 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1659 "Remove from default list?",
\r
1660 "Remove user defined colour",
\r
1661 JOptionPane.YES_NO_OPTION);
\r
1662 if(option == JOptionPane.YES_OPTION)
\r
1664 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1665 colourMenu.remove(radioItem);
\r
1668 radioItem.addActionListener(new ActionListener()
\r
1670 public void actionPerformed(ActionEvent evt)
\r
1672 userDefinedColour_actionPerformed(evt);
\r
1678 radioItem.addActionListener(new ActionListener()
\r
1680 public void actionPerformed(ActionEvent evt)
\r
1682 userDefinedColour_actionPerformed(evt);
\r
1686 colourMenu.insert(radioItem, 15);
\r
1687 colours.add(radioItem);
\r
1695 * @param e DOCUMENT ME!
\r
1697 public void PIDColour_actionPerformed(ActionEvent e)
\r
1699 changeColour(new PIDColourScheme());
\r
1705 * @param e DOCUMENT ME!
\r
1707 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1709 changeColour(new Blosum62ColourScheme());
\r
1715 * @param e DOCUMENT ME!
\r
1717 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1719 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1720 HistoryItem.SORT));
\r
1721 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1722 viewport.getAlignment().getSequenceAt(0));
\r
1723 alignPanel.repaint();
\r
1729 * @param e DOCUMENT ME!
\r
1731 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1733 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1734 HistoryItem.SORT));
\r
1735 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1736 alignPanel.repaint();
\r
1742 * @param e DOCUMENT ME!
\r
1744 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1746 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1747 HistoryItem.SORT));
\r
1749 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1750 alignPanel.repaint();
\r
1756 * @param e DOCUMENT ME!
\r
1758 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1760 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1761 JInternalFrame frame = new JInternalFrame();
\r
1762 frame.setContentPane(sp);
\r
1763 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1770 * @param e DOCUMENT ME!
\r
1772 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1774 if ( (viewport.getSelectionGroup() == null) ||
\r
1775 (viewport.getSelectionGroup().getSize() < 2))
\r
1777 JOptionPane.showInternalMessageDialog(this,
\r
1778 "You must select at least 2 sequences.",
\r
1779 "Invalid Selection",
\r
1780 JOptionPane.WARNING_MESSAGE);
\r
1784 JInternalFrame frame = new JInternalFrame();
\r
1785 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1786 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1793 * @param e DOCUMENT ME!
\r
1795 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1797 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1798 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1799 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1800 (viewport.getAlignment().getHeight() < 4))
\r
1802 JOptionPane.showInternalMessageDialog(this,
\r
1803 "Principal component analysis must take\n" +
\r
1804 "at least 4 input sequences.",
\r
1805 "Sequence selection insufficient",
\r
1806 JOptionPane.WARNING_MESSAGE);
\r
1813 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1814 JInternalFrame frame = new JInternalFrame();
\r
1815 frame.setContentPane(pcaPanel);
\r
1816 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1819 catch (java.lang.OutOfMemoryError ex)
\r
1821 JOptionPane.showInternalMessageDialog(this,
\r
1822 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1824 JOptionPane.WARNING_MESSAGE);
\r
1831 * @param e DOCUMENT ME!
\r
1833 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1835 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1841 * @param e DOCUMENT ME!
\r
1843 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1845 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1851 * @param e DOCUMENT ME!
\r
1853 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1855 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1861 * @param e DOCUMENT ME!
\r
1863 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1865 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1871 * @param type DOCUMENT ME!
\r
1872 * @param pwType DOCUMENT ME!
\r
1873 * @param title DOCUMENT ME!
\r
1875 void NewTreePanel(String type, String pwType, String title)
\r
1877 final TreePanel tp;
\r
1879 if ( (viewport.getSelectionGroup() != null) &&
\r
1880 (viewport.getSelectionGroup().getSize() > 3))
\r
1883 SequenceGroup sg = viewport.getSelectionGroup();
\r
1885 /* Decide if the selection is a column region */
\r
1886 while (s < sg.sequences.size())
\r
1888 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1891 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1892 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1893 "Try using the Pad function in the edit menu,\n" +
\r
1894 "or one of the multiple sequence alignment web services.",
\r
1895 "Sequences in selection are not aligned",
\r
1896 JOptionPane.WARNING_MESSAGE);
\r
1902 title = title + " on region";
\r
1903 tp = new TreePanel(viewport,
\r
1904 viewport.getSelectionGroup().sequences, type, pwType,
\r
1905 sg.getStartRes(), sg.getEndRes());
\r
1909 //are the sequences aligned?
\r
1910 if (!viewport.alignment.isAligned())
\r
1912 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1913 "The sequences must be aligned before creating a tree.\n" +
\r
1914 "Try using the Pad function in the edit menu,\n" +
\r
1915 "or one of the multiple sequence alignment web services.",
\r
1916 "Sequences not aligned",
\r
1917 JOptionPane.WARNING_MESSAGE);
\r
1922 tp = new TreePanel(viewport,
\r
1923 viewport.getAlignment().getSequences(), type, pwType,
\r
1925 viewport.alignment.getWidth());
\r
1928 addTreeMenuItem(tp, title);
\r
1929 viewport.setCurrentTree(tp.getTree());
\r
1931 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1937 * @param title DOCUMENT ME!
\r
1938 * @param order DOCUMENT ME!
\r
1940 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1942 final JMenuItem item = new JMenuItem("by " + title);
\r
1944 item.addActionListener(new java.awt.event.ActionListener()
\r
1946 public void actionPerformed(ActionEvent e)
\r
1948 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1949 HistoryItem.SORT));
\r
1951 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1952 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1953 alignPanel.repaint();
\r
1959 * Maintain the Order by->Displayed Tree menu.
\r
1960 * Creates a new menu item for a TreePanel with an appropriate
\r
1961 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
1962 * to remove the menu item when the treePanel is closed, and adjust
\r
1963 * the tree leaf to sequence mapping when the alignment is modified.
\r
1964 * @param treePanel Displayed tree window.
\r
1965 * @param title SortBy menu item title.
\r
1967 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1969 final JMenuItem item = new JMenuItem(title);
\r
1973 if (treeCount == 1)
\r
1975 sort.add(sortByTreeMenu);
\r
1978 sortByTreeMenu.add(item);
\r
1979 item.addActionListener(new java.awt.event.ActionListener()
\r
1981 public void actionPerformed(ActionEvent e)
\r
1983 addHistoryItem(new HistoryItem("Tree Sort",
\r
1984 viewport.alignment, HistoryItem.SORT));
\r
1985 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1986 treePanel.getTree());
\r
1987 alignPanel.repaint();
\r
1991 treePanel.addInternalFrameListener(new javax.swing.event.
\r
1992 InternalFrameAdapter()
\r
1994 public void internalFrameClosed(
\r
1995 javax.swing.event.InternalFrameEvent evt)
\r
1998 sortByTreeMenu.remove(item);
\r
2000 if (treeCount == 0)
\r
2002 sort.remove(sortByTreeMenu);
\r
2007 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
2009 public void propertyChange(PropertyChangeEvent evt)
\r
2011 if (evt.getPropertyName().equals("alignment"))
\r
2013 treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
2014 treePanel.repaint();
\r
2021 * Work out whether the whole set of sequences
\r
2022 * or just the selected set will be submitted for multiple alignment.
\r
2025 private SequenceI[] gatherSequencesForAlignment()
\r
2027 // Now, check we have enough sequences
\r
2028 SequenceI[] msa = null;
\r
2030 if ( (viewport.getSelectionGroup() != null) &&
\r
2031 (viewport.getSelectionGroup().getSize() > 1))
\r
2033 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2034 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2036 msa = new SequenceI[sz = seqs.getSize()];
\r
2038 for (int i = 0; i < sz; i++)
\r
2040 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2045 Vector seqs = viewport.getAlignment().getSequences();
\r
2047 if (seqs.size() > 1)
\r
2049 msa = new SequenceI[seqs.size()];
\r
2051 for (int i = 0; i < seqs.size(); i++)
\r
2053 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2061 * Decides what is submitted to a secondary structure prediction service,
\r
2062 * the currently selected sequence, or the currently selected alignment
\r
2063 * (where the first sequence in the set is the one that the prediction
\r
2066 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2068 SequenceI seq = null;
\r
2069 SequenceI[] msa = null;
\r
2071 if ( (viewport.getSelectionGroup() != null) &&
\r
2072 (viewport.getSelectionGroup().getSize() > 0))
\r
2074 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2075 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2077 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2079 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2084 msa = new SequenceI[sz = seqs.getSize()];
\r
2086 for (int i = 0; i < sz; i++)
\r
2088 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2094 Vector seqs = viewport.getAlignment().getSequences();
\r
2096 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2098 seq = (SequenceI) seqs.elementAt(0);
\r
2102 msa = new SequenceI[seqs.size()];
\r
2104 for (int i = 0; i < seqs.size(); i++)
\r
2106 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2118 return new SequenceI[]
\r
2128 * @param e DOCUMENT ME!
\r
2130 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2132 // Pick the tree file
\r
2133 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2135 "LAST_DIRECTORY"));
\r
2136 chooser.setFileView(new JalviewFileView());
\r
2137 chooser.setDialogTitle("Select a newick-like tree file");
\r
2138 chooser.setToolTipText("Load a tree file");
\r
2140 int value = chooser.showOpenDialog(null);
\r
2142 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2144 String choice = chooser.getSelectedFile().getPath();
\r
2145 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2149 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2151 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2153 catch (Exception ex)
\r
2155 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2156 "Problem reading tree file",
\r
2158 JOptionPane.WARNING_MESSAGE);
\r
2159 ex.printStackTrace();
\r
2165 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2167 return ShowNewickTree(nf,title,600,500,4,5);
\r
2172 * @param nf DOCUMENT ME!
\r
2173 * @param title DOCUMENT ME!
\r
2175 * @return DOCUMENT ME!
\r
2177 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2179 TreePanel tp = null;
\r
2185 if (nf.getTree() != null)
\r
2187 tp = new TreePanel(viewport,
\r
2188 viewport.getAlignment().getSequences(), nf,
\r
2195 tp.setLocation(x,y);
\r
2198 Desktop.addInternalFrame(tp, title, w, h);
\r
2199 addTreeMenuItem(tp, title);
\r
2202 catch (Exception ex)
\r
2204 ex.printStackTrace();
\r
2215 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2216 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2217 printJob.setPrintable(alignPanel, pf);
\r
2219 if (printJob.printDialog())
\r
2225 catch (Exception PrintException)
\r
2227 PrintException.printStackTrace();
\r
2234 * Generates menu items and listener event actions for web service clients
\r
2237 public void BuildWebServiceMenu()
\r
2239 if ( (Desktop.discoverer.services != null)
\r
2240 && (Desktop.discoverer.services.size() > 0))
\r
2242 Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
\r
2243 Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
\r
2244 Vector wsmenu = new Vector();
\r
2245 if (msaws != null)
\r
2247 // Add any Multiple Sequence Alignment Services
\r
2248 final JMenu msawsmenu = new JMenu("Alignment");
\r
2249 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2251 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2253 final JMenuItem method = new JMenuItem(sh.getName());
\r
2254 method.addActionListener(new ActionListener()
\r
2256 public void actionPerformed(ActionEvent e)
\r
2258 SequenceI[] msa = gatherSequencesForAlignment();
\r
2259 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2265 msawsmenu.add(method);
\r
2266 // Deal with services that we know accept partial alignments.
\r
2267 if (sh.getName().indexOf("lustal") > -1)
\r
2269 // We know that ClustalWS can accept partial alignments for refinement.
\r
2270 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2271 methodR.addActionListener(new ActionListener()
\r
2273 public void actionPerformed(ActionEvent e)
\r
2275 SequenceI[] msa = gatherSequencesForAlignment();
\r
2276 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2282 msawsmenu.add(methodR);
\r
2286 wsmenu.add(msawsmenu);
\r
2288 if (secstrpr != null)
\r
2290 // Add any secondary structure prediction services
\r
2291 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2292 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2294 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2296 final JMenuItem method = new JMenuItem(sh.getName());
\r
2297 method.addActionListener(new ActionListener()
\r
2299 public void actionPerformed(ActionEvent e)
\r
2301 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2302 if (msa.length == 1)
\r
2304 // Single Sequence prediction
\r
2305 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2310 if (msa.length > 1)
\r
2312 // Single Sequence prediction
\r
2313 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2319 secstrmenu.add(method);
\r
2321 wsmenu.add(secstrmenu);
\r
2323 this.webService.removeAll();
\r
2324 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2326 webService.add( (JMenu) wsmenu.get(i));
\r
2331 this.webService.removeAll();
\r
2332 this.webService.add(this.webServiceNoServices);
\r
2334 // TODO: add in rediscovery function
\r
2335 // TODO: reduce code redundancy.
\r
2336 // TODO: group services by location as well as function.
\r