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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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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242 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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243 currentFileFormat);
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245 String choice = chooser.getSelectedFile().getPath();
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246 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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248 saveAlignment(choice, currentFileFormat);
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252 public boolean saveAlignment(String file, String format)
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254 if (format.equalsIgnoreCase("Jalview"))
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256 String shortName = title;
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258 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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260 shortName = shortName.substring(shortName.lastIndexOf(
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261 java.io.File.separatorChar) + 1);
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264 Jalview2XML.SaveAlignment(this, file, shortName);
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266 // USE Jalview2XML to save this file
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271 String output = FormatAdapter.formatSequences(format,
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272 viewport.getAlignment().
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274 if (output == null)
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281 java.io.PrintWriter out = new java.io.PrintWriter(
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282 new java.io.FileWriter(file));
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288 catch (Exception ex)
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290 ex.printStackTrace();
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299 * @param e DOCUMENT ME!
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301 protected void outputText_actionPerformed(ActionEvent e)
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303 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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304 Desktop.addInternalFrame(cap,
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305 "Alignment output - " + e.getActionCommand(), 600,
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307 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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308 viewport.getAlignment().
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315 * @param e DOCUMENT ME!
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317 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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319 new HTMLOutput(viewport);
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322 public void createImageMap(File file, String image)
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324 alignPanel.makePNGImageMap(file, image);
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330 * @param e DOCUMENT ME!
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332 public void createPNG(File f)
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334 alignPanel.makePNG(f);
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340 * @param e DOCUMENT ME!
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342 public void createEPS(File f)
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344 alignPanel.makeEPS(f);
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350 * @param e DOCUMENT ME!
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352 public void printMenuItem_actionPerformed(ActionEvent e)
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354 //Putting in a thread avoids Swing painting problems
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355 PrintThread thread = new PrintThread();
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362 * @param e DOCUMENT ME!
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364 public void closeMenuItem_actionPerformed(ActionEvent e)
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368 PaintRefresher.components.remove(viewport.alignment);
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369 this.setClosed(true);
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371 catch (Exception ex)
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379 void updateEditMenuBar()
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381 if (historyList.size() > 0)
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383 undoMenuItem.setEnabled(true);
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385 HistoryItem hi = (HistoryItem) historyList.peek();
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386 undoMenuItem.setText("Undo " + hi.getDescription());
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390 undoMenuItem.setEnabled(false);
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391 undoMenuItem.setText("Undo");
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394 if (redoList.size() > 0)
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396 redoMenuItem.setEnabled(true);
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398 HistoryItem hi = (HistoryItem) redoList.peek();
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399 redoMenuItem.setText("Redo " + hi.getDescription());
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403 redoMenuItem.setEnabled(false);
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404 redoMenuItem.setText("Redo");
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411 * @param hi DOCUMENT ME!
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413 public void addHistoryItem(HistoryItem hi)
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415 historyList.push(hi);
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416 updateEditMenuBar();
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422 * @param e DOCUMENT ME!
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424 protected void undoMenuItem_actionPerformed(ActionEvent e)
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426 HistoryItem hi = (HistoryItem) historyList.pop();
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427 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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428 HistoryItem.HIDE));
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429 restoreHistoryItem(hi);
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430 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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436 * @param e DOCUMENT ME!
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438 protected void redoMenuItem_actionPerformed(ActionEvent e)
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440 HistoryItem hi = (HistoryItem) redoList.pop();
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441 restoreHistoryItem(hi);
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442 updateEditMenuBar();
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443 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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446 // used by undo and redo
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447 void restoreHistoryItem(HistoryItem hi)
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449 if (hi.getType() == HistoryItem.SORT)
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451 for (int i = 0; i < hi.getSequences().size(); i++)
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453 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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460 for (int i = 0; i < hi.getSequences().size(); i++)
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462 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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464 if (restore.getLength() == 0)
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466 restore.setSequence(hi.getHidden().elementAt(i).toString());
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467 viewport.alignment.getSequences().insertElementAt(restore,
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468 hi.getAlignIndex(i));
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472 restore.setSequence(hi.getHidden().elementAt(i).toString());
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476 if (hi.getType() == HistoryItem.PASTE)
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478 for (int i = viewport.alignment.getHeight() - 1;
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479 i > (hi.getSequences().size() - 1); i--)
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481 viewport.alignment.deleteSequence(i);
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486 updateEditMenuBar();
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488 viewport.firePropertyChange("alignment", null,
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489 viewport.getAlignment().getSequences());
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495 * @param up DOCUMENT ME!
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497 public void moveSelectedSequences(boolean up)
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499 SequenceGroup sg = viewport.getSelectionGroup();
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508 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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510 SequenceI seq = viewport.alignment.getSequenceAt(i);
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512 if (!sg.sequences.contains(seq))
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517 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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519 if (sg.sequences.contains(temp))
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524 viewport.alignment.getSequences().setElementAt(temp, i);
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525 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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530 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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532 SequenceI seq = viewport.alignment.getSequenceAt(i);
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534 if (!sg.sequences.contains(seq))
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539 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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541 if (sg.sequences.contains(temp))
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546 viewport.alignment.getSequences().setElementAt(temp, i);
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547 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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551 alignPanel.repaint();
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557 * @param e DOCUMENT ME!
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559 protected void copy_actionPerformed(ActionEvent e)
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561 if (viewport.getSelectionGroup() == null)
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563 System.out.println("null here");
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567 SequenceGroup sg = viewport.getSelectionGroup();
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569 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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571 Hashtable orderedSeqs = new Hashtable();
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572 SequenceI [] seqs = new SequenceI[sg.getSize()];
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574 for (int i = 0; i < sg.getSize(); i++)
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576 SequenceI seq = sg.getSequenceAt(i);
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577 int index = viewport.alignment.findIndex(seq);
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578 orderedSeqs.put(index + "", seq);
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581 int index = 0, startRes, endRes;
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584 for (int i = 0; i < sg.getSize(); i++)
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586 SequenceI seq = null;
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588 while (seq == null)
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590 if (orderedSeqs.containsKey(index + ""))
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592 seq = (SequenceI) orderedSeqs.get(index + "");
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605 //Returns residue following index if gap
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606 startRes = seq.findPosition(sg.getStartRes());
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609 //Need to find the residue preceeding index if gap
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612 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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614 ch = seq.getCharAt(j);
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615 if (!jalview.util.Comparison.isGap( (ch)))
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623 endRes += seq.getStart() - 1;
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626 seqs[i] = new Sequence(seq.getName(),
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627 seq.getSequence(sg.getStartRes(), sg.getEndRes()+1),
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632 System.out.println("BLOBL"+FastaFile.print(seqs));
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634 c.setContents(new StringSelection(FastaFile.print(seqs)), null);
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640 * @param e DOCUMENT ME!
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642 protected void pasteNew_actionPerformed(ActionEvent e)
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650 * @param e DOCUMENT ME!
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652 protected void pasteThis_actionPerformed(ActionEvent e)
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654 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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655 HistoryItem.PASTE));
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662 * @param newAlignment DOCUMENT ME!
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664 void paste(boolean newAlignment)
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668 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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669 Transferable contents = c.getContents(this);
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671 if (contents == null)
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676 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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678 String format = IdentifyFile.Identify(str, "Paste");
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679 SequenceI[] sequences = FormatAdapter.readFile(str, "Paste", format);
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684 AlignFrame af = new AlignFrame(new Alignment(sequences));
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685 String newtitle = new String("Copied sequences");
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687 if (title.startsWith("Copied sequences"))
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693 newtitle = newtitle.concat("- from " + title);
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696 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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697 NEW_WINDOW_HEIGHT);
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702 for (int i = 0; i < sequences.length; i++)
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703 viewport.alignment.addSequence(sequences[i]);
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705 viewport.setEndSeq(viewport.alignment.getHeight());
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706 viewport.alignment.getWidth();
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707 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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710 catch (Exception ex)
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712 // could be anything being pasted in here
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721 * @param e DOCUMENT ME!
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723 protected void cut_actionPerformed(ActionEvent e)
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725 copy_actionPerformed(null);
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726 delete_actionPerformed(null);
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732 * @param e DOCUMENT ME!
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734 protected void delete_actionPerformed(ActionEvent e)
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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 viewport.getAlignment().deleteSequence(seq);
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771 viewport.getAlignment().getSequences().setElementAt(seq, index);
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775 viewport.setSelectionGroup(null);
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776 viewport.alignment.deleteGroup(sg);
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778 viewport.firePropertyChange("alignment", null,
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779 viewport.getAlignment().getSequences());
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783 if (viewport.getAlignment().getHeight() < 1)
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787 this.setClosed(true);
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789 catch (Exception ex)
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798 * @param e DOCUMENT ME!
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800 protected void deleteGroups_actionPerformed(ActionEvent e)
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802 viewport.alignment.deleteAllGroups();
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803 viewport.setSelectionGroup(null);
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804 alignPanel.repaint();
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810 * @param e DOCUMENT ME!
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812 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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814 SequenceGroup sg = new SequenceGroup();
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816 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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819 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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822 sg.setEndRes(viewport.alignment.getWidth() - 1);
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823 viewport.setSelectionGroup(sg);
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824 PaintRefresher.Refresh(null, viewport.alignment);
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830 * @param e DOCUMENT ME!
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832 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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834 viewport.setSelectionGroup(null);
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835 viewport.getColumnSelection().clear();
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836 viewport.setSelectionGroup(null);
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837 alignPanel.annotationPanel.activeRes = null;
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838 PaintRefresher.Refresh(null, viewport.alignment);
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844 * @param e DOCUMENT ME!
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846 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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848 SequenceGroup sg = viewport.getSelectionGroup();
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852 selectAllSequenceMenuItem_actionPerformed(null);
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857 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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860 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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863 PaintRefresher.Refresh(null, viewport.alignment);
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869 * @param e DOCUMENT ME!
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871 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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873 ColumnSelection colSel = viewport.getColumnSelection();
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875 if (colSel.size() > 0)
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877 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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878 HistoryItem.HIDE));
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880 int min = colSel.getMin();
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881 viewport.getAlignment().trimLeft(min);
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882 colSel.compensateForEdit(0, min);
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884 if (viewport.getSelectionGroup() != null)
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886 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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889 Vector groups = viewport.alignment.getGroups();
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891 for (int i = 0; i < groups.size(); i++)
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893 SequenceGroup sg = (SequenceGroup) groups.get(i);
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895 if (!sg.adjustForRemoveLeft(min))
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897 viewport.alignment.deleteGroup(sg);
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901 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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908 * @param e DOCUMENT ME!
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910 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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912 ColumnSelection colSel = viewport.getColumnSelection();
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914 if (colSel.size() > 0)
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916 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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917 HistoryItem.HIDE));
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919 int max = colSel.getMax();
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920 viewport.getAlignment().trimRight(max);
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922 if (viewport.getSelectionGroup() != null)
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924 viewport.getSelectionGroup().adjustForRemoveRight(max);
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927 Vector groups = viewport.alignment.getGroups();
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929 for (int i = 0; i < groups.size(); i++)
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931 SequenceGroup sg = (SequenceGroup) groups.get(i);
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933 if (!sg.adjustForRemoveRight(max))
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935 viewport.alignment.deleteGroup(sg);
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939 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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946 * @param e DOCUMENT ME!
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948 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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950 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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951 viewport.alignment, HistoryItem.HIDE));
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953 //This is to maintain viewport position on first residue
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954 //of first sequence
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955 SequenceI seq = viewport.alignment.getSequenceAt(0);
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956 int startRes = seq.findPosition(viewport.startRes);
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958 viewport.getAlignment().removeGaps();
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960 viewport.setStartRes(seq.findIndex(startRes)-1);
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962 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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968 * @param e DOCUMENT ME!
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970 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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972 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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973 HistoryItem.HIDE));
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975 //This is to maintain viewport position on first residue
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976 //of first sequence
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977 SequenceI seq = viewport.alignment.getSequenceAt(0);
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978 int startRes = seq.findPosition(viewport.startRes);
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984 Vector seqs = null;
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987 int end = viewport.alignment.getWidth();
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989 if (viewport.getSelectionGroup() != null
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990 && viewport.getSelectionGroup().sequences != null
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991 && viewport.getSelectionGroup().sequences.size() > 0)
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993 seqs = viewport.getSelectionGroup().sequences;
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994 start = viewport.getSelectionGroup().getStartRes();
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995 end = viewport.getSelectionGroup().getEndRes()+1;
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999 seqs = viewport.alignment.getSequences();
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1002 for (int i = 0; i < seqs.size(); i++)
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1004 current = (SequenceI) seqs.elementAt(i);
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1005 jSize = current.getLength();
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1007 // Removing a range is much quicker than removing gaps
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1008 // one by one for long sequences
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1010 int rangeStart=-1, rangeEnd=-1;
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1014 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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1016 if(rangeStart==-1)
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1031 current.deleteChars(rangeStart, rangeEnd);
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1032 j-=rangeEnd-rangeStart;
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1033 jSize-=rangeEnd-rangeStart;
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1041 while (j < end && j < jSize);
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1044 current.deleteChars(rangeStart, rangeEnd);
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1048 viewport.setStartRes(seq.findIndex(startRes)-1);
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1050 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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1053 public void alignmentChanged()
\r
1055 if(viewport.vconsensus!=null)
\r
1057 viewport.updateConsensus();
\r
1058 viewport.updateConservation();
\r
1060 resetAllColourSchemes();
\r
1061 if(alignPanel.overviewPanel!=null)
\r
1062 alignPanel.overviewPanel.updateOverviewImage();
\r
1064 alignPanel.repaint();
\r
1067 void resetAllColourSchemes()
\r
1069 ColourSchemeI cs = viewport.globalColourScheme;
\r
1072 if (cs instanceof ClustalxColourScheme)
\r
1074 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1075 resetClustalX(viewport.alignment.getSequences(),
\r
1076 viewport.alignment.getWidth());
\r
1079 cs.setConsensus(viewport.vconsensus);
\r
1080 if (cs.conservationApplied())
\r
1082 Alignment al = (Alignment) viewport.alignment;
\r
1083 Conservation c = new Conservation("All",
\r
1084 ResidueProperties.propHash, 3,
\r
1085 al.getSequences(), 0,
\r
1086 al.getWidth() - 1);
\r
1088 c.verdict(false, viewport.ConsPercGaps);
\r
1090 cs.setConservation(c);
\r
1094 int s, sSize = viewport.alignment.getGroups().size();
\r
1095 for(s=0; s<sSize; s++)
\r
1097 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1098 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1100 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1102 sg.recalcConservation();
\r
1109 * @param e DOCUMENT ME!
\r
1111 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1113 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1114 HistoryItem.HIDE));
\r
1116 SequenceI current;
\r
1117 int Width = viewport.getAlignment().getWidth();
\r
1119 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1122 current = viewport.getAlignment().getSequenceAt(i);
\r
1124 if (current.getLength() < Width)
\r
1126 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1130 alignmentChanged();
\r
1136 * @param e DOCUMENT ME!
\r
1138 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1140 JInternalFrame frame = new JInternalFrame();
\r
1141 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1142 frame.setContentPane(finder);
\r
1143 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1144 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1150 * @param e DOCUMENT ME!
\r
1152 public void font_actionPerformed(ActionEvent e)
\r
1154 FontChooser fc = new FontChooser(alignPanel);
\r
1160 * @param e DOCUMENT ME!
\r
1162 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1164 viewport.setShowFullId(fullSeqId.isSelected());
\r
1166 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1167 alignPanel.repaint();
\r
1173 * @param e DOCUMENT ME!
\r
1175 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1177 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1178 alignPanel.repaint();
\r
1184 * @param e DOCUMENT ME!
\r
1186 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1188 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1189 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1190 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1191 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1192 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1193 alignPanel.repaint();
\r
1199 * @param e DOCUMENT ME!
\r
1201 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1203 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1204 alignPanel.repaint();
\r
1210 * @param e DOCUMENT ME!
\r
1212 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1214 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1215 alignPanel.repaint();
\r
1221 * @param e DOCUMENT ME!
\r
1223 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1225 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1226 alignPanel.repaint();
\r
1232 * @param e DOCUMENT ME!
\r
1234 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1236 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1237 alignPanel.repaint();
\r
1243 * @param e DOCUMENT ME!
\r
1245 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1247 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1248 alignPanel.repaint();
\r
1254 * @param e DOCUMENT ME!
\r
1256 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1258 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1259 alignPanel.repaint();
\r
1265 * @param evt DOCUMENT ME!
\r
1267 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1269 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1271 if (viewport.showSequenceFeatures &&
\r
1272 ! ( (Alignment) viewport.alignment).featuresAdded)
\r
1274 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
\r
1277 ( (Alignment) viewport.alignment).featuresAdded = true;
\r
1280 alignPanel.repaint();
\r
1286 * @param e DOCUMENT ME!
\r
1288 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1290 if (annotationPanelMenuItem.isSelected() &&
\r
1291 viewport.getWrapAlignment())
\r
1293 annotationPanelMenuItem.setSelected(false);
\r
1298 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1299 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1305 * @param e DOCUMENT ME!
\r
1307 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1309 if (alignPanel.overviewPanel != null)
\r
1314 JInternalFrame frame = new JInternalFrame();
\r
1315 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1316 frame.setContentPane(overview);
\r
1317 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1318 frame.getWidth(), frame.getHeight());
\r
1320 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1321 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1323 public void internalFrameClosed(
\r
1324 javax.swing.event.InternalFrameEvent evt)
\r
1326 alignPanel.setOverviewPanel(null);
\r
1331 alignPanel.setOverviewPanel(overview);
\r
1337 * @param e DOCUMENT ME!
\r
1339 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1341 changeColour(null);
\r
1347 * @param e DOCUMENT ME!
\r
1349 public void clustalColour_actionPerformed(ActionEvent e)
\r
1351 changeColour(new ClustalxColourScheme(
\r
1352 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1358 * @param e DOCUMENT ME!
\r
1360 public void zappoColour_actionPerformed(ActionEvent e)
\r
1362 changeColour(new ZappoColourScheme());
\r
1368 * @param e DOCUMENT ME!
\r
1370 public void taylorColour_actionPerformed(ActionEvent e)
\r
1372 changeColour(new TaylorColourScheme());
\r
1378 * @param e DOCUMENT ME!
\r
1380 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1382 changeColour(new HydrophobicColourScheme());
\r
1388 * @param e DOCUMENT ME!
\r
1390 public void helixColour_actionPerformed(ActionEvent e)
\r
1392 changeColour(new HelixColourScheme());
\r
1398 * @param e DOCUMENT ME!
\r
1400 public void strandColour_actionPerformed(ActionEvent e)
\r
1402 changeColour(new StrandColourScheme());
\r
1408 * @param e DOCUMENT ME!
\r
1410 public void turnColour_actionPerformed(ActionEvent e)
\r
1412 changeColour(new TurnColourScheme());
\r
1418 * @param e DOCUMENT ME!
\r
1420 public void buriedColour_actionPerformed(ActionEvent e)
\r
1422 changeColour(new BuriedColourScheme());
\r
1428 * @param e DOCUMENT ME!
\r
1430 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1432 changeColour(new NucleotideColourScheme());
\r
1438 * @param e DOCUMENT ME!
\r
1440 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1442 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1448 * @param cs DOCUMENT ME!
\r
1450 void changeColour(ColourSchemeI cs)
\r
1452 int threshold = 0;
\r
1456 if (viewport.getAbovePIDThreshold())
\r
1458 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1461 cs.setThreshold(threshold,
\r
1462 viewport.getIgnoreGapsConsensus());
\r
1464 viewport.setGlobalColourScheme(cs);
\r
1468 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1471 if (viewport.getConservationSelected())
\r
1474 Alignment al = (Alignment) viewport.alignment;
\r
1475 Conservation c = new Conservation("All",
\r
1476 ResidueProperties.propHash, 3,
\r
1477 al.getSequences(), 0,
\r
1478 al.getWidth() - 1);
\r
1481 c.verdict(false, viewport.ConsPercGaps);
\r
1483 cs.setConservation(c);
\r
1485 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1490 cs.setConservation(null);
\r
1493 cs.setConsensus(viewport.vconsensus);
\r
1496 viewport.setGlobalColourScheme(cs);
\r
1498 if (viewport.getColourAppliesToAllGroups())
\r
1500 Vector groups = viewport.alignment.getGroups();
\r
1502 for (int i = 0; i < groups.size(); i++)
\r
1504 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1512 if (cs instanceof ClustalxColourScheme)
\r
1514 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1516 else if (cs instanceof UserColourScheme)
\r
1518 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1524 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1526 catch (Exception ex)
\r
1531 if (viewport.getAbovePIDThreshold()
\r
1532 || cs instanceof PIDColourScheme
\r
1533 || cs instanceof Blosum62ColourScheme)
\r
1535 sg.cs.setThreshold(threshold,
\r
1536 viewport.getIgnoreGapsConsensus());
\r
1538 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1542 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1545 if (viewport.getConservationSelected())
\r
1547 Conservation c = new Conservation("Group",
\r
1548 ResidueProperties.propHash, 3,
\r
1550 viewport.alignment.getWidth() - 1);
\r
1552 c.verdict(false, viewport.ConsPercGaps);
\r
1553 sg.cs.setConservation(c);
\r
1556 sg.cs.setConservation(null);
\r
1560 if (alignPanel.getOverviewPanel() != null)
\r
1562 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1565 alignPanel.repaint();
\r
1571 * @param e DOCUMENT ME!
\r
1573 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1575 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1577 SliderPanel.setPIDSliderSource(alignPanel,
\r
1578 viewport.getGlobalColourScheme(),
\r
1580 SliderPanel.showPIDSlider();
\r
1587 * @param e DOCUMENT ME!
\r
1589 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1591 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1593 SliderPanel.setConservationSlider(alignPanel,
\r
1594 viewport.globalColourScheme,
\r
1596 SliderPanel.showConservationSlider();
\r
1603 * @param e DOCUMENT ME!
\r
1605 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1607 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1609 viewport.setAbovePIDThreshold(false);
\r
1610 abovePIDThreshold.setSelected(false);
\r
1612 changeColour(viewport.getGlobalColourScheme());
\r
1614 modifyConservation_actionPerformed(null);
\r
1620 * @param e DOCUMENT ME!
\r
1622 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1624 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1626 conservationMenuItem.setSelected(false);
\r
1627 viewport.setConservationSelected(false);
\r
1629 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1631 changeColour(viewport.getGlobalColourScheme());
\r
1633 modifyPID_actionPerformed(null);
\r
1639 * @param e DOCUMENT ME!
\r
1641 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1643 if (e.getActionCommand().equals("User Defined..."))
\r
1645 new UserDefinedColours(alignPanel, null);
\r
1649 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1650 getUserColourSchemes().get(e.getActionCommand());
\r
1652 changeColour(udc);
\r
1656 public void updateUserColourMenu()
\r
1659 Component[] menuItems = colourMenu.getMenuComponents();
\r
1660 int i, iSize = menuItems.length;
\r
1661 for (i = 0; i < iSize; i++)
\r
1663 if (menuItems[i].getName() != null &&
\r
1664 menuItems[i].getName().equals("USER_DEFINED"))
\r
1666 colourMenu.remove(menuItems[i]);
\r
1670 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1672 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1673 getUserColourSchemes().keys();
\r
1675 while (userColours.hasMoreElements())
\r
1677 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1678 nextElement().toString());
\r
1679 radioItem.setName("USER_DEFINED");
\r
1680 radioItem.addMouseListener(new MouseAdapter()
\r
1682 public void mousePressed(MouseEvent evt)
\r
1684 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1686 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1688 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1689 "Remove from default list?",
\r
1690 "Remove user defined colour",
\r
1691 JOptionPane.YES_NO_OPTION);
\r
1692 if(option == JOptionPane.YES_OPTION)
\r
1694 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1695 colourMenu.remove(radioItem);
\r
1698 radioItem.addActionListener(new ActionListener()
\r
1700 public void actionPerformed(ActionEvent evt)
\r
1702 userDefinedColour_actionPerformed(evt);
\r
1708 radioItem.addActionListener(new ActionListener()
\r
1710 public void actionPerformed(ActionEvent evt)
\r
1712 userDefinedColour_actionPerformed(evt);
\r
1716 colourMenu.insert(radioItem, 15);
\r
1717 colours.add(radioItem);
\r
1725 * @param e DOCUMENT ME!
\r
1727 public void PIDColour_actionPerformed(ActionEvent e)
\r
1729 changeColour(new PIDColourScheme());
\r
1735 * @param e DOCUMENT ME!
\r
1737 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1739 changeColour(new Blosum62ColourScheme());
\r
1745 * @param e DOCUMENT ME!
\r
1747 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1749 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1750 HistoryItem.SORT));
\r
1751 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1752 viewport.getAlignment().getSequenceAt(0));
\r
1753 alignPanel.repaint();
\r
1759 * @param e DOCUMENT ME!
\r
1761 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1763 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1764 HistoryItem.SORT));
\r
1765 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1766 alignPanel.repaint();
\r
1772 * @param e DOCUMENT ME!
\r
1774 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1776 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1777 HistoryItem.SORT));
\r
1779 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1780 alignPanel.repaint();
\r
1786 * @param e DOCUMENT ME!
\r
1788 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1790 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1791 JInternalFrame frame = new JInternalFrame();
\r
1792 frame.setContentPane(sp);
\r
1793 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1800 * @param e DOCUMENT ME!
\r
1802 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1804 if ( (viewport.getSelectionGroup() == null) ||
\r
1805 (viewport.getSelectionGroup().getSize() < 2))
\r
1807 JOptionPane.showInternalMessageDialog(this,
\r
1808 "You must select at least 2 sequences.",
\r
1809 "Invalid Selection",
\r
1810 JOptionPane.WARNING_MESSAGE);
\r
1814 JInternalFrame frame = new JInternalFrame();
\r
1815 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1816 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1823 * @param e DOCUMENT ME!
\r
1825 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1827 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1828 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1829 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1830 (viewport.getAlignment().getHeight() < 4))
\r
1832 JOptionPane.showInternalMessageDialog(this,
\r
1833 "Principal component analysis must take\n" +
\r
1834 "at least 4 input sequences.",
\r
1835 "Sequence selection insufficient",
\r
1836 JOptionPane.WARNING_MESSAGE);
\r
1841 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1842 JInternalFrame frame = new JInternalFrame();
\r
1843 frame.setContentPane(pcaPanel);
\r
1844 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1851 * @param e DOCUMENT ME!
\r
1853 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1855 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1861 * @param e DOCUMENT ME!
\r
1863 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1865 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1871 * @param e DOCUMENT ME!
\r
1873 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1875 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1881 * @param e DOCUMENT ME!
\r
1883 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1885 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1891 * @param type DOCUMENT ME!
\r
1892 * @param pwType DOCUMENT ME!
\r
1893 * @param title DOCUMENT ME!
\r
1895 void NewTreePanel(String type, String pwType, String title)
\r
1897 final TreePanel tp;
\r
1899 if ( (viewport.getSelectionGroup() != null) &&
\r
1900 (viewport.getSelectionGroup().getSize() > 3))
\r
1903 SequenceGroup sg = viewport.getSelectionGroup();
\r
1905 /* Decide if the selection is a column region */
\r
1906 while (s < sg.sequences.size())
\r
1908 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1911 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1912 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1913 "Try using the Pad function in the edit menu,\n" +
\r
1914 "or one of the multiple sequence alignment web services.",
\r
1915 "Sequences in selection are not aligned",
\r
1916 JOptionPane.WARNING_MESSAGE);
\r
1922 title = title + " on region";
\r
1923 tp = new TreePanel(viewport,
\r
1924 viewport.getSelectionGroup().sequences, type, pwType,
\r
1925 sg.getStartRes(), sg.getEndRes());
\r
1929 //are the sequences aligned?
\r
1930 if (!viewport.alignment.isAligned())
\r
1932 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1933 "The sequences must be aligned before creating a tree.\n" +
\r
1934 "Try using the Pad function in the edit menu,\n" +
\r
1935 "or one of the multiple sequence alignment web services.",
\r
1936 "Sequences not aligned",
\r
1937 JOptionPane.WARNING_MESSAGE);
\r
1942 tp = new TreePanel(viewport,
\r
1943 viewport.getAlignment().getSequences(), type, pwType,
\r
1945 viewport.alignment.getWidth());
\r
1948 addTreeMenuItem(tp, title);
\r
1949 viewport.setCurrentTree(tp.getTree());
\r
1951 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1957 * @param title DOCUMENT ME!
\r
1958 * @param order DOCUMENT ME!
\r
1960 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1962 final JMenuItem item = new JMenuItem("by " + title);
\r
1964 item.addActionListener(new java.awt.event.ActionListener()
\r
1966 public void actionPerformed(ActionEvent e)
\r
1968 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1969 HistoryItem.SORT));
\r
1971 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1972 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1973 alignPanel.repaint();
\r
1979 * Maintain the Order by->Displayed Tree menu.
\r
1980 * Creates a new menu item for a TreePanel with an appropriate
\r
1981 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
1982 * to remove the menu item when the treePanel is closed, and adjust
\r
1983 * the tree leaf to sequence mapping when the alignment is modified.
\r
1984 * @param treePanel Displayed tree window.
\r
1985 * @param title SortBy menu item title.
\r
1987 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1989 final JMenuItem item = new JMenuItem(title);
\r
1993 if (treeCount == 1)
\r
1995 sort.add(sortByTreeMenu);
\r
1998 sortByTreeMenu.add(item);
\r
1999 item.addActionListener(new java.awt.event.ActionListener()
\r
2001 public void actionPerformed(ActionEvent e)
\r
2003 addHistoryItem(new HistoryItem("Tree Sort",
\r
2004 viewport.alignment, HistoryItem.SORT));
\r
2005 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2006 treePanel.getTree());
\r
2007 alignPanel.repaint();
\r
2011 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2012 InternalFrameAdapter()
\r
2014 public void internalFrameClosed(
\r
2015 javax.swing.event.InternalFrameEvent evt)
\r
2018 sortByTreeMenu.remove(item);
\r
2020 if (treeCount == 0)
\r
2022 sort.remove(sortByTreeMenu);
\r
2030 * Work out whether the whole set of sequences
\r
2031 * or just the selected set will be submitted for multiple alignment.
\r
2034 private SequenceI[] gatherSequencesForAlignment()
\r
2036 // Now, check we have enough sequences
\r
2037 SequenceI[] msa = null;
\r
2039 if ( (viewport.getSelectionGroup() != null) &&
\r
2040 (viewport.getSelectionGroup().getSize() > 1))
\r
2042 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2043 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2045 msa = new SequenceI[sz = seqs.getSize()];
\r
2047 for (int i = 0; i < sz; i++)
\r
2049 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2054 Vector seqs = viewport.getAlignment().getSequences();
\r
2056 if (seqs.size() > 1)
\r
2058 msa = new SequenceI[seqs.size()];
\r
2060 for (int i = 0; i < seqs.size(); i++)
\r
2062 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2070 * Decides what is submitted to a secondary structure prediction service,
\r
2071 * the currently selected sequence, or the currently selected alignment
\r
2072 * (where the first sequence in the set is the one that the prediction
\r
2075 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2077 SequenceI seq = null;
\r
2078 SequenceI[] msa = null;
\r
2080 if ( (viewport.getSelectionGroup() != null) &&
\r
2081 (viewport.getSelectionGroup().getSize() > 0))
\r
2083 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2084 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2086 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2088 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2093 msa = new SequenceI[sz = seqs.getSize()];
\r
2095 for (int i = 0; i < sz; i++)
\r
2097 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2103 Vector seqs = viewport.getAlignment().getSequences();
\r
2105 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2107 seq = (SequenceI) seqs.elementAt(0);
\r
2111 msa = new SequenceI[seqs.size()];
\r
2113 for (int i = 0; i < seqs.size(); i++)
\r
2115 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2127 return new SequenceI[]
\r
2137 * @param e DOCUMENT ME!
\r
2139 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2141 // Pick the tree file
\r
2142 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2144 "LAST_DIRECTORY"));
\r
2145 chooser.setFileView(new JalviewFileView());
\r
2146 chooser.setDialogTitle("Select a newick-like tree file");
\r
2147 chooser.setToolTipText("Load a tree file");
\r
2149 int value = chooser.showOpenDialog(null);
\r
2151 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2153 String choice = chooser.getSelectedFile().getPath();
\r
2154 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2158 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2160 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2162 catch (Exception ex)
\r
2164 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2165 "Problem reading tree file",
\r
2167 JOptionPane.WARNING_MESSAGE);
\r
2168 ex.printStackTrace();
\r
2174 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2176 return ShowNewickTree(nf,title,600,500,4,5);
\r
2181 * @param nf DOCUMENT ME!
\r
2182 * @param title DOCUMENT ME!
\r
2184 * @return DOCUMENT ME!
\r
2186 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2188 TreePanel tp = null;
\r
2194 if (nf.getTree() != null)
\r
2196 tp = new TreePanel(viewport,
\r
2197 viewport.getAlignment().getSequences(), nf,
\r
2204 tp.setLocation(x,y);
\r
2207 Desktop.addInternalFrame(tp, title, w, h);
\r
2208 addTreeMenuItem(tp, title);
\r
2211 catch (Exception ex)
\r
2213 ex.printStackTrace();
\r
2224 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2225 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2226 printJob.setPrintable(alignPanel, pf);
\r
2228 if (printJob.printDialog())
\r
2234 catch (Exception PrintException)
\r
2236 PrintException.printStackTrace();
\r
2243 * Generates menu items and listener event actions for web service clients
\r
2246 public void BuildWebServiceMenu()
\r
2248 if ( (Desktop.discoverer.services != null)
\r
2249 && (Desktop.discoverer.services.size() > 0))
\r
2251 Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
\r
2252 Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
\r
2253 Vector wsmenu = new Vector();
\r
2254 if (msaws != null)
\r
2256 // Add any Multiple Sequence Alignment Services
\r
2257 final JMenu msawsmenu = new JMenu("Alignment");
\r
2258 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2260 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2262 final JMenuItem method = new JMenuItem(sh.getName());
\r
2263 method.addActionListener(new ActionListener()
\r
2265 public void actionPerformed(ActionEvent e)
\r
2267 SequenceI[] msa = gatherSequencesForAlignment();
\r
2268 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2274 msawsmenu.add(method);
\r
2275 // Deal with services that we know accept partial alignments.
\r
2276 if (sh.getName().indexOf("lustal") > -1)
\r
2278 // We know that ClustalWS can accept partial alignments for refinement.
\r
2279 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2280 methodR.addActionListener(new ActionListener()
\r
2282 public void actionPerformed(ActionEvent e)
\r
2284 SequenceI[] msa = gatherSequencesForAlignment();
\r
2285 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2291 msawsmenu.add(methodR);
\r
2295 wsmenu.add(msawsmenu);
\r
2297 if (secstrpr != null)
\r
2299 // Add any secondary structure prediction services
\r
2300 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2301 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2303 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2305 final JMenuItem method = new JMenuItem(sh.getName());
\r
2306 method.addActionListener(new ActionListener()
\r
2308 public void actionPerformed(ActionEvent e)
\r
2310 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2311 if (msa.length == 1)
\r
2313 // Single Sequence prediction
\r
2314 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2319 if (msa.length > 1)
\r
2321 // Single Sequence prediction
\r
2322 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2328 secstrmenu.add(method);
\r
2330 wsmenu.add(secstrmenu);
\r
2332 this.webService.removeAll();
\r
2333 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2335 webService.add( (JMenu) wsmenu.get(i));
\r
2340 this.webService.removeAll();
\r
2341 this.webService.add(this.webServiceNoServices);
\r
2343 // TODO: add in rediscovery function
\r
2344 // TODO: reduce code redundancy.
\r
2345 // TODO: group services by location as well as function.
\r