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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566 SequenceGroup sg = viewport.getSelectionGroup();
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568 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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569 StringBuffer buffer = new StringBuffer();
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571 Hashtable orderedSeqs = new Hashtable();
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573 for (int i = 0; i < sg.getSize(); i++)
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575 SequenceI seq = sg.getSequenceAt(i);
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576 int index = viewport.alignment.findIndex(seq);
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577 orderedSeqs.put(index + "", seq);
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580 int index = 0, startRes, endRes;
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583 for (int i = 0; i < sg.getSize(); i++)
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585 SequenceI seq = null;
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587 while (seq == null)
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589 if (orderedSeqs.containsKey(index + ""))
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591 seq = (SequenceI) orderedSeqs.get(index + "");
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602 //Returns residue following index if gap
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603 startRes = seq.findPosition(sg.getStartRes());
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606 //Need to find the residue preceeding index if gap
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609 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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611 ch = seq.getCharAt(j);
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612 if (!jalview.util.Comparison.isGap( (ch)))
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620 endRes += seq.getStart() - 1;
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623 buffer.append(seq.getName() + "\t" +
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626 seq.getSequence(sg.getStartRes(),
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627 sg.getEndRes() + 1) + "\n");
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630 c.setContents(new StringSelection(buffer.toString()), null);
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636 * @param e DOCUMENT ME!
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638 protected void pasteNew_actionPerformed(ActionEvent e)
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646 * @param e DOCUMENT ME!
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648 protected void pasteThis_actionPerformed(ActionEvent e)
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650 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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651 HistoryItem.PASTE));
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658 * @param newAlignment DOCUMENT ME!
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660 void paste(boolean newAlignment)
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664 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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665 Transferable contents = c.getContents(this);
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667 if (contents == null)
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672 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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673 StringTokenizer st = new StringTokenizer(str);
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674 ArrayList seqs = new ArrayList();
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676 while (st.hasMoreElements())
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678 String name = st.nextToken();
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679 int start = Integer.parseInt(st.nextToken());
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680 int end = Integer.parseInt(st.nextToken());
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681 Sequence sequence = new Sequence(name, st.nextToken(), start,
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686 viewport.alignment.addSequence(sequence);
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690 seqs.add(sequence);
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696 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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697 seqs.toArray(newSeqs);
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699 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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700 String newtitle = new String("Copied sequences");
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702 if (title.startsWith("Copied sequences"))
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708 newtitle = newtitle.concat("- from " + title);
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711 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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712 NEW_WINDOW_HEIGHT);
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716 viewport.setEndSeq(viewport.alignment.getHeight());
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717 viewport.alignment.getWidth();
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718 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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721 catch (Exception ex)
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723 // could be anything being pasted in here
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732 * @param e DOCUMENT ME!
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734 protected void cut_actionPerformed(ActionEvent e)
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736 copy_actionPerformed(null);
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737 delete_actionPerformed(null);
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743 * @param e DOCUMENT ME!
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745 protected void delete_actionPerformed(ActionEvent e)
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748 if (viewport.getSelectionGroup() == null)
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753 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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754 HistoryItem.HIDE));
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756 SequenceGroup sg = viewport.getSelectionGroup();
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757 boolean allSequences = false;
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758 if (sg.sequences.size() == viewport.alignment.getHeight())
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760 allSequences = true;
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763 for (int i = 0; i < sg.sequences.size(); i++)
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765 SequenceI seq = sg.getSequenceAt(i);
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766 int index = viewport.getAlignment().findIndex(seq);
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767 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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769 // If the cut affects all sequences, remove highlighted columns
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772 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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773 sg.getEndRes() + 1);
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776 if (seq.getSequence().length() < 1)
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778 viewport.getAlignment().deleteSequence(seq);
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782 viewport.getAlignment().getSequences().setElementAt(seq, index);
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786 viewport.setSelectionGroup(null);
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787 viewport.alignment.deleteGroup(sg);
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789 viewport.firePropertyChange("alignment", null,
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790 viewport.getAlignment().getSequences());
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794 if (viewport.getAlignment().getHeight() < 1)
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798 this.setClosed(true);
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800 catch (Exception ex)
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809 * @param e DOCUMENT ME!
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811 protected void deleteGroups_actionPerformed(ActionEvent e)
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813 viewport.alignment.deleteAllGroups();
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814 viewport.setSelectionGroup(null);
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815 alignPanel.repaint();
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821 * @param e DOCUMENT ME!
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823 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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825 SequenceGroup sg = new SequenceGroup();
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827 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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830 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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833 sg.setEndRes(viewport.alignment.getWidth() - 1);
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834 viewport.setSelectionGroup(sg);
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835 PaintRefresher.Refresh(null, viewport.alignment);
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841 * @param e DOCUMENT ME!
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843 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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845 viewport.setSelectionGroup(null);
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846 viewport.getColumnSelection().clear();
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847 viewport.setSelectionGroup(null);
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848 alignPanel.annotationPanel.activeRes = null;
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849 PaintRefresher.Refresh(null, viewport.alignment);
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855 * @param e DOCUMENT ME!
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857 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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859 SequenceGroup sg = viewport.getSelectionGroup();
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863 selectAllSequenceMenuItem_actionPerformed(null);
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868 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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871 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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874 PaintRefresher.Refresh(null, viewport.alignment);
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880 * @param e DOCUMENT ME!
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882 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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884 ColumnSelection colSel = viewport.getColumnSelection();
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886 if (colSel.size() > 0)
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888 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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889 HistoryItem.HIDE));
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891 int min = colSel.getMin();
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892 viewport.getAlignment().trimLeft(min);
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893 colSel.compensateForEdit(0, min);
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895 if (viewport.getSelectionGroup() != null)
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897 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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900 Vector groups = viewport.alignment.getGroups();
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902 for (int i = 0; i < groups.size(); i++)
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904 SequenceGroup sg = (SequenceGroup) groups.get(i);
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906 if (!sg.adjustForRemoveLeft(min))
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908 viewport.alignment.deleteGroup(sg);
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912 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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919 * @param e DOCUMENT ME!
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921 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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923 ColumnSelection colSel = viewport.getColumnSelection();
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925 if (colSel.size() > 0)
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927 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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928 HistoryItem.HIDE));
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930 int max = colSel.getMax();
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931 viewport.getAlignment().trimRight(max);
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933 if (viewport.getSelectionGroup() != null)
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935 viewport.getSelectionGroup().adjustForRemoveRight(max);
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938 Vector groups = viewport.alignment.getGroups();
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940 for (int i = 0; i < groups.size(); i++)
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942 SequenceGroup sg = (SequenceGroup) groups.get(i);
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944 if (!sg.adjustForRemoveRight(max))
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946 viewport.alignment.deleteGroup(sg);
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950 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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957 * @param e DOCUMENT ME!
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959 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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961 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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962 viewport.alignment, HistoryItem.HIDE));
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964 //This is to maintain viewport position on first residue
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965 //of first sequence
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966 SequenceI seq = viewport.alignment.getSequenceAt(0);
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967 int startRes = seq.findPosition(viewport.startRes);
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969 viewport.getAlignment().removeGaps();
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971 viewport.setStartRes(seq.findIndex(startRes)-1);
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973 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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979 * @param e DOCUMENT ME!
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981 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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983 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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984 HistoryItem.HIDE));
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986 //This is to maintain viewport position on first residue
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987 //of first sequence
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988 SequenceI seq = viewport.alignment.getSequenceAt(0);
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989 int startRes = seq.findPosition(viewport.startRes);
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995 Vector seqs = null;
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998 int end = viewport.alignment.getWidth();
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1000 if (viewport.getSelectionGroup() != null
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1001 && viewport.getSelectionGroup().sequences != null
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1002 && viewport.getSelectionGroup().sequences.size() > 0)
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1004 seqs = viewport.getSelectionGroup().sequences;
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1005 start = viewport.getSelectionGroup().getStartRes();
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1006 end = viewport.getSelectionGroup().getEndRes()+1;
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1010 seqs = viewport.alignment.getSequences();
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1013 for (int i = 0; i < seqs.size(); i++)
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1015 current = (SequenceI) seqs.elementAt(i);
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1016 jSize = current.getLength();
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1018 // Removing a range is much quicker than removing gaps
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1019 // one by one for long sequences
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1021 int rangeStart=-1, rangeEnd=-1;
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1025 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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1027 if(rangeStart==-1)
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1042 current.deleteChars(rangeStart, rangeEnd);
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1043 j-=rangeEnd-rangeStart;
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1044 jSize-=rangeEnd-rangeStart;
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1052 while (j < end && j < jSize);
\r
1055 current.deleteChars(rangeStart, rangeEnd);
\r
1059 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
1061 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
1064 public void alignmentChanged()
\r
1066 if(viewport.vconsensus!=null)
\r
1068 viewport.updateConsensus();
\r
1069 viewport.updateConservation();
\r
1071 resetAllColourSchemes();
\r
1072 if(alignPanel.overviewPanel!=null)
\r
1073 alignPanel.overviewPanel.updateOverviewImage();
\r
1075 alignPanel.repaint();
\r
1078 void resetAllColourSchemes()
\r
1080 ColourSchemeI cs = viewport.globalColourScheme;
\r
1083 if (cs instanceof ClustalxColourScheme)
\r
1085 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1086 resetClustalX(viewport.alignment.getSequences(),
\r
1087 viewport.alignment.getWidth());
\r
1090 cs.setConsensus(viewport.vconsensus);
\r
1091 if (cs.conservationApplied())
\r
1093 Alignment al = (Alignment) viewport.alignment;
\r
1094 Conservation c = new Conservation("All",
\r
1095 ResidueProperties.propHash, 3,
\r
1096 al.getSequences(), 0,
\r
1097 al.getWidth() - 1);
\r
1099 c.verdict(false, viewport.ConsPercGaps);
\r
1101 cs.setConservation(c);
\r
1105 int s, sSize = viewport.alignment.getGroups().size();
\r
1106 for(s=0; s<sSize; s++)
\r
1108 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1109 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1111 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1113 sg.recalcConservation();
\r
1120 * @param e DOCUMENT ME!
\r
1122 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1124 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1125 HistoryItem.HIDE));
\r
1127 SequenceI current;
\r
1128 int Width = viewport.getAlignment().getWidth();
\r
1130 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1133 current = viewport.getAlignment().getSequenceAt(i);
\r
1135 if (current.getLength() < Width)
\r
1137 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1141 alignmentChanged();
\r
1147 * @param e DOCUMENT ME!
\r
1149 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1151 JInternalFrame frame = new JInternalFrame();
\r
1152 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1153 frame.setContentPane(finder);
\r
1154 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1155 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1161 * @param e DOCUMENT ME!
\r
1163 public void font_actionPerformed(ActionEvent e)
\r
1165 FontChooser fc = new FontChooser(alignPanel);
\r
1171 * @param e DOCUMENT ME!
\r
1173 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1175 viewport.setShowFullId(fullSeqId.isSelected());
\r
1177 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1178 alignPanel.repaint();
\r
1184 * @param e DOCUMENT ME!
\r
1186 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1188 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1189 alignPanel.repaint();
\r
1195 * @param e DOCUMENT ME!
\r
1197 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1199 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1200 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1201 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1202 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1203 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1204 alignPanel.repaint();
\r
1210 * @param e DOCUMENT ME!
\r
1212 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1214 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1215 alignPanel.repaint();
\r
1221 * @param e DOCUMENT ME!
\r
1223 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1225 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1226 alignPanel.repaint();
\r
1232 * @param e DOCUMENT ME!
\r
1234 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1236 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1237 alignPanel.repaint();
\r
1243 * @param e DOCUMENT ME!
\r
1245 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1247 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1248 alignPanel.repaint();
\r
1254 * @param e DOCUMENT ME!
\r
1256 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1258 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1259 alignPanel.repaint();
\r
1265 * @param e DOCUMENT ME!
\r
1267 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1269 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1270 alignPanel.repaint();
\r
1276 * @param evt DOCUMENT ME!
\r
1278 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1280 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1282 if (viewport.showSequenceFeatures &&
\r
1283 ! ( (Alignment) viewport.alignment).featuresAdded)
\r
1285 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
\r
1288 ( (Alignment) viewport.alignment).featuresAdded = true;
\r
1291 alignPanel.repaint();
\r
1297 * @param e DOCUMENT ME!
\r
1299 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1301 if (annotationPanelMenuItem.isSelected() &&
\r
1302 viewport.getWrapAlignment())
\r
1304 annotationPanelMenuItem.setSelected(false);
\r
1309 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1310 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1316 * @param e DOCUMENT ME!
\r
1318 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1320 if (alignPanel.overviewPanel != null)
\r
1325 JInternalFrame frame = new JInternalFrame();
\r
1326 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1327 frame.setContentPane(overview);
\r
1328 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1329 frame.getWidth(), frame.getHeight());
\r
1331 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1332 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1334 public void internalFrameClosed(
\r
1335 javax.swing.event.InternalFrameEvent evt)
\r
1337 alignPanel.setOverviewPanel(null);
\r
1342 alignPanel.setOverviewPanel(overview);
\r
1348 * @param e DOCUMENT ME!
\r
1350 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1352 changeColour(null);
\r
1358 * @param e DOCUMENT ME!
\r
1360 public void clustalColour_actionPerformed(ActionEvent e)
\r
1362 changeColour(new ClustalxColourScheme(
\r
1363 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1369 * @param e DOCUMENT ME!
\r
1371 public void zappoColour_actionPerformed(ActionEvent e)
\r
1373 changeColour(new ZappoColourScheme());
\r
1379 * @param e DOCUMENT ME!
\r
1381 public void taylorColour_actionPerformed(ActionEvent e)
\r
1383 changeColour(new TaylorColourScheme());
\r
1389 * @param e DOCUMENT ME!
\r
1391 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1393 changeColour(new HydrophobicColourScheme());
\r
1399 * @param e DOCUMENT ME!
\r
1401 public void helixColour_actionPerformed(ActionEvent e)
\r
1403 changeColour(new HelixColourScheme());
\r
1409 * @param e DOCUMENT ME!
\r
1411 public void strandColour_actionPerformed(ActionEvent e)
\r
1413 changeColour(new StrandColourScheme());
\r
1419 * @param e DOCUMENT ME!
\r
1421 public void turnColour_actionPerformed(ActionEvent e)
\r
1423 changeColour(new TurnColourScheme());
\r
1429 * @param e DOCUMENT ME!
\r
1431 public void buriedColour_actionPerformed(ActionEvent e)
\r
1433 changeColour(new BuriedColourScheme());
\r
1439 * @param e DOCUMENT ME!
\r
1441 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1443 changeColour(new NucleotideColourScheme());
\r
1449 * @param e DOCUMENT ME!
\r
1451 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1453 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1459 * @param cs DOCUMENT ME!
\r
1461 void changeColour(ColourSchemeI cs)
\r
1463 int threshold = 0;
\r
1467 if (viewport.getAbovePIDThreshold())
\r
1469 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1472 cs.setThreshold(threshold,
\r
1473 viewport.getIgnoreGapsConsensus());
\r
1475 viewport.setGlobalColourScheme(cs);
\r
1479 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1482 if (viewport.getConservationSelected())
\r
1485 Alignment al = (Alignment) viewport.alignment;
\r
1486 Conservation c = new Conservation("All",
\r
1487 ResidueProperties.propHash, 3,
\r
1488 al.getSequences(), 0,
\r
1489 al.getWidth() - 1);
\r
1492 c.verdict(false, viewport.ConsPercGaps);
\r
1494 cs.setConservation(c);
\r
1496 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1501 cs.setConservation(null);
\r
1504 cs.setConsensus(viewport.vconsensus);
\r
1507 viewport.setGlobalColourScheme(cs);
\r
1509 if (viewport.getColourAppliesToAllGroups())
\r
1511 Vector groups = viewport.alignment.getGroups();
\r
1513 for (int i = 0; i < groups.size(); i++)
\r
1515 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1523 if (cs instanceof ClustalxColourScheme)
\r
1525 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1527 else if (cs instanceof UserColourScheme)
\r
1529 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1535 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1537 catch (Exception ex)
\r
1542 if (viewport.getAbovePIDThreshold()
\r
1543 || cs instanceof PIDColourScheme
\r
1544 || cs instanceof Blosum62ColourScheme)
\r
1546 sg.cs.setThreshold(threshold,
\r
1547 viewport.getIgnoreGapsConsensus());
\r
1549 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1553 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1556 if (viewport.getConservationSelected())
\r
1558 Conservation c = new Conservation("Group",
\r
1559 ResidueProperties.propHash, 3,
\r
1561 viewport.alignment.getWidth() - 1);
\r
1563 c.verdict(false, viewport.ConsPercGaps);
\r
1564 sg.cs.setConservation(c);
\r
1567 sg.cs.setConservation(null);
\r
1571 if (alignPanel.getOverviewPanel() != null)
\r
1573 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1576 alignPanel.repaint();
\r
1582 * @param e DOCUMENT ME!
\r
1584 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1586 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1588 SliderPanel.setPIDSliderSource(alignPanel,
\r
1589 viewport.getGlobalColourScheme(),
\r
1591 SliderPanel.showPIDSlider();
\r
1598 * @param e DOCUMENT ME!
\r
1600 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1602 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1604 SliderPanel.setConservationSlider(alignPanel,
\r
1605 viewport.globalColourScheme,
\r
1607 SliderPanel.showConservationSlider();
\r
1614 * @param e DOCUMENT ME!
\r
1616 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1618 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1620 viewport.setAbovePIDThreshold(false);
\r
1621 abovePIDThreshold.setSelected(false);
\r
1623 changeColour(viewport.getGlobalColourScheme());
\r
1625 modifyConservation_actionPerformed(null);
\r
1631 * @param e DOCUMENT ME!
\r
1633 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1635 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1637 conservationMenuItem.setSelected(false);
\r
1638 viewport.setConservationSelected(false);
\r
1640 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1642 changeColour(viewport.getGlobalColourScheme());
\r
1644 modifyPID_actionPerformed(null);
\r
1650 * @param e DOCUMENT ME!
\r
1652 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1654 if (e.getActionCommand().equals("User Defined..."))
\r
1656 new UserDefinedColours(alignPanel, null);
\r
1660 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1661 getUserColourSchemes().get(e.getActionCommand());
\r
1663 changeColour(udc);
\r
1667 public void updateUserColourMenu()
\r
1670 Component[] menuItems = colourMenu.getMenuComponents();
\r
1671 int i, iSize = menuItems.length;
\r
1672 for (i = 0; i < iSize; i++)
\r
1674 if (menuItems[i].getName() != null &&
\r
1675 menuItems[i].getName().equals("USER_DEFINED"))
\r
1677 colourMenu.remove(menuItems[i]);
\r
1681 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1683 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1684 getUserColourSchemes().keys();
\r
1686 while (userColours.hasMoreElements())
\r
1688 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1689 nextElement().toString());
\r
1690 radioItem.setName("USER_DEFINED");
\r
1691 radioItem.addMouseListener(new MouseAdapter()
\r
1693 public void mousePressed(MouseEvent evt)
\r
1695 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1697 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1699 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1700 "Remove from default list?",
\r
1701 "Remove user defined colour",
\r
1702 JOptionPane.YES_NO_OPTION);
\r
1703 if(option == JOptionPane.YES_OPTION)
\r
1705 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1706 colourMenu.remove(radioItem);
\r
1709 radioItem.addActionListener(new ActionListener()
\r
1711 public void actionPerformed(ActionEvent evt)
\r
1713 userDefinedColour_actionPerformed(evt);
\r
1719 radioItem.addActionListener(new ActionListener()
\r
1721 public void actionPerformed(ActionEvent evt)
\r
1723 userDefinedColour_actionPerformed(evt);
\r
1727 colourMenu.insert(radioItem, 15);
\r
1728 colours.add(radioItem);
\r
1736 * @param e DOCUMENT ME!
\r
1738 public void PIDColour_actionPerformed(ActionEvent e)
\r
1740 changeColour(new PIDColourScheme());
\r
1746 * @param e DOCUMENT ME!
\r
1748 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1750 changeColour(new Blosum62ColourScheme());
\r
1756 * @param e DOCUMENT ME!
\r
1758 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1760 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1761 HistoryItem.SORT));
\r
1762 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1763 viewport.getAlignment().getSequenceAt(0));
\r
1764 alignPanel.repaint();
\r
1770 * @param e DOCUMENT ME!
\r
1772 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1774 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1775 HistoryItem.SORT));
\r
1776 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1777 alignPanel.repaint();
\r
1783 * @param e DOCUMENT ME!
\r
1785 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1787 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1788 HistoryItem.SORT));
\r
1790 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1791 alignPanel.repaint();
\r
1797 * @param e DOCUMENT ME!
\r
1799 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1801 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1802 JInternalFrame frame = new JInternalFrame();
\r
1803 frame.setContentPane(sp);
\r
1804 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1811 * @param e DOCUMENT ME!
\r
1813 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1815 if ( (viewport.getSelectionGroup() == null) ||
\r
1816 (viewport.getSelectionGroup().getSize() < 2))
\r
1818 JOptionPane.showInternalMessageDialog(this,
\r
1819 "You must select at least 2 sequences.",
\r
1820 "Invalid Selection",
\r
1821 JOptionPane.WARNING_MESSAGE);
\r
1825 JInternalFrame frame = new JInternalFrame();
\r
1826 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1827 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1834 * @param e DOCUMENT ME!
\r
1836 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1838 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1839 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1840 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1841 (viewport.getAlignment().getHeight() < 4))
\r
1843 JOptionPane.showInternalMessageDialog(this,
\r
1844 "Principal component analysis must take\n" +
\r
1845 "at least 4 input sequences.",
\r
1846 "Sequence selection insufficient",
\r
1847 JOptionPane.WARNING_MESSAGE);
\r
1852 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1853 JInternalFrame frame = new JInternalFrame();
\r
1854 frame.setContentPane(pcaPanel);
\r
1855 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1862 * @param e DOCUMENT ME!
\r
1864 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1866 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1872 * @param e DOCUMENT ME!
\r
1874 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1876 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1882 * @param e DOCUMENT ME!
\r
1884 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1886 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1892 * @param e DOCUMENT ME!
\r
1894 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1896 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1902 * @param type DOCUMENT ME!
\r
1903 * @param pwType DOCUMENT ME!
\r
1904 * @param title DOCUMENT ME!
\r
1906 void NewTreePanel(String type, String pwType, String title)
\r
1908 final TreePanel tp;
\r
1910 if ( (viewport.getSelectionGroup() != null) &&
\r
1911 (viewport.getSelectionGroup().getSize() > 3))
\r
1914 SequenceGroup sg = viewport.getSelectionGroup();
\r
1916 /* Decide if the selection is a column region */
\r
1917 while (s < sg.sequences.size())
\r
1919 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1922 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1923 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1924 "Try using the Pad function in the edit menu,\n" +
\r
1925 "or one of the multiple sequence alignment web services.",
\r
1926 "Sequences in selection are not aligned",
\r
1927 JOptionPane.WARNING_MESSAGE);
\r
1933 title = title + " on region";
\r
1934 tp = new TreePanel(viewport,
\r
1935 viewport.getSelectionGroup().sequences, type, pwType,
\r
1936 sg.getStartRes(), sg.getEndRes());
\r
1940 //are the sequences aligned?
\r
1941 if (!viewport.alignment.isAligned())
\r
1943 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1944 "The sequences must be aligned before creating a tree.\n" +
\r
1945 "Try using the Pad function in the edit menu,\n" +
\r
1946 "or one of the multiple sequence alignment web services.",
\r
1947 "Sequences not aligned",
\r
1948 JOptionPane.WARNING_MESSAGE);
\r
1953 tp = new TreePanel(viewport,
\r
1954 viewport.getAlignment().getSequences(), type, pwType,
\r
1956 viewport.alignment.getWidth());
\r
1959 addTreeMenuItem(tp, title);
\r
1960 viewport.setCurrentTree(tp.getTree());
\r
1962 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1968 * @param title DOCUMENT ME!
\r
1969 * @param order DOCUMENT ME!
\r
1971 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1973 final JMenuItem item = new JMenuItem("by " + title);
\r
1975 item.addActionListener(new java.awt.event.ActionListener()
\r
1977 public void actionPerformed(ActionEvent e)
\r
1979 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1980 HistoryItem.SORT));
\r
1982 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1983 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1984 alignPanel.repaint();
\r
1990 * Maintain the Order by->Displayed Tree menu.
\r
1991 * Creates a new menu item for a TreePanel with an appropriate
\r
1992 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
1993 * to remove the menu item when the treePanel is closed, and adjust
\r
1994 * the tree leaf to sequence mapping when the alignment is modified.
\r
1995 * @param treePanel Displayed tree window.
\r
1996 * @param title SortBy menu item title.
\r
1998 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
2000 final JMenuItem item = new JMenuItem(title);
\r
2004 if (treeCount == 1)
\r
2006 sort.add(sortByTreeMenu);
\r
2009 sortByTreeMenu.add(item);
\r
2010 item.addActionListener(new java.awt.event.ActionListener()
\r
2012 public void actionPerformed(ActionEvent e)
\r
2014 addHistoryItem(new HistoryItem("Tree Sort",
\r
2015 viewport.alignment, HistoryItem.SORT));
\r
2016 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
2017 treePanel.getTree());
\r
2018 alignPanel.repaint();
\r
2022 treePanel.addInternalFrameListener(new javax.swing.event.
\r
2023 InternalFrameAdapter()
\r
2025 public void internalFrameClosed(
\r
2026 javax.swing.event.InternalFrameEvent evt)
\r
2029 sortByTreeMenu.remove(item);
\r
2031 if (treeCount == 0)
\r
2033 sort.remove(sortByTreeMenu);
\r
2041 * Work out whether the whole set of sequences
\r
2042 * or just the selected set will be submitted for multiple alignment.
\r
2045 private SequenceI[] gatherSequencesForAlignment()
\r
2047 // Now, check we have enough sequences
\r
2048 SequenceI[] msa = null;
\r
2050 if ( (viewport.getSelectionGroup() != null) &&
\r
2051 (viewport.getSelectionGroup().getSize() > 1))
\r
2053 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2054 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2056 msa = new SequenceI[sz = seqs.getSize()];
\r
2058 for (int i = 0; i < sz; i++)
\r
2060 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2065 Vector seqs = viewport.getAlignment().getSequences();
\r
2067 if (seqs.size() > 1)
\r
2069 msa = new SequenceI[seqs.size()];
\r
2071 for (int i = 0; i < seqs.size(); i++)
\r
2073 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2081 * Decides what is submitted to a secondary structure prediction service,
\r
2082 * the currently selected sequence, or the currently selected alignment
\r
2083 * (where the first sequence in the set is the one that the prediction
\r
2086 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2088 SequenceI seq = null;
\r
2089 SequenceI[] msa = null;
\r
2091 if ( (viewport.getSelectionGroup() != null) &&
\r
2092 (viewport.getSelectionGroup().getSize() > 0))
\r
2094 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2095 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2097 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2099 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2104 msa = new SequenceI[sz = seqs.getSize()];
\r
2106 for (int i = 0; i < sz; i++)
\r
2108 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2114 Vector seqs = viewport.getAlignment().getSequences();
\r
2116 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2118 seq = (SequenceI) seqs.elementAt(0);
\r
2122 msa = new SequenceI[seqs.size()];
\r
2124 for (int i = 0; i < seqs.size(); i++)
\r
2126 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2138 return new SequenceI[]
\r
2148 * @param e DOCUMENT ME!
\r
2150 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2152 // Pick the tree file
\r
2153 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2155 "LAST_DIRECTORY"));
\r
2156 chooser.setFileView(new JalviewFileView());
\r
2157 chooser.setDialogTitle("Select a newick-like tree file");
\r
2158 chooser.setToolTipText("Load a tree file");
\r
2160 int value = chooser.showOpenDialog(null);
\r
2162 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2164 String choice = chooser.getSelectedFile().getPath();
\r
2165 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2169 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2171 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2173 catch (Exception ex)
\r
2175 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2176 "Problem reading tree file",
\r
2178 JOptionPane.WARNING_MESSAGE);
\r
2179 ex.printStackTrace();
\r
2185 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2187 return ShowNewickTree(nf,title,600,500,4,5);
\r
2192 * @param nf DOCUMENT ME!
\r
2193 * @param title DOCUMENT ME!
\r
2195 * @return DOCUMENT ME!
\r
2197 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2199 TreePanel tp = null;
\r
2205 if (nf.getTree() != null)
\r
2207 tp = new TreePanel(viewport,
\r
2208 viewport.getAlignment().getSequences(), nf,
\r
2215 tp.setLocation(x,y);
\r
2218 Desktop.addInternalFrame(tp, title, w, h);
\r
2219 addTreeMenuItem(tp, title);
\r
2222 catch (Exception ex)
\r
2224 ex.printStackTrace();
\r
2235 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2236 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2237 printJob.setPrintable(alignPanel, pf);
\r
2239 if (printJob.printDialog())
\r
2245 catch (Exception PrintException)
\r
2247 PrintException.printStackTrace();
\r
2254 * Generates menu items and listener event actions for web service clients
\r
2257 public void BuildWebServiceMenu()
\r
2259 if ( (Desktop.discoverer.services != null)
\r
2260 && (Desktop.discoverer.services.size() > 0))
\r
2262 Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
\r
2263 Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
\r
2264 Vector wsmenu = new Vector();
\r
2265 if (msaws != null)
\r
2267 // Add any Multiple Sequence Alignment Services
\r
2268 final JMenu msawsmenu = new JMenu("Alignment");
\r
2269 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2271 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2273 final JMenuItem method = new JMenuItem(sh.getName());
\r
2274 method.addActionListener(new ActionListener()
\r
2276 public void actionPerformed(ActionEvent e)
\r
2278 SequenceI[] msa = gatherSequencesForAlignment();
\r
2279 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2285 msawsmenu.add(method);
\r
2286 // Deal with services that we know accept partial alignments.
\r
2287 if (sh.getName().indexOf("lustal") > -1)
\r
2289 // We know that ClustalWS can accept partial alignments for refinement.
\r
2290 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2291 methodR.addActionListener(new ActionListener()
\r
2293 public void actionPerformed(ActionEvent e)
\r
2295 SequenceI[] msa = gatherSequencesForAlignment();
\r
2296 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2302 msawsmenu.add(methodR);
\r
2306 wsmenu.add(msawsmenu);
\r
2308 if (secstrpr != null)
\r
2310 // Add any secondary structure prediction services
\r
2311 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2312 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2314 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2316 final JMenuItem method = new JMenuItem(sh.getName());
\r
2317 method.addActionListener(new ActionListener()
\r
2319 public void actionPerformed(ActionEvent e)
\r
2321 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2322 if (msa.length == 1)
\r
2324 // Single Sequence prediction
\r
2325 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2330 if (msa.length > 1)
\r
2332 // Single Sequence prediction
\r
2333 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2339 secstrmenu.add(method);
\r
2341 wsmenu.add(secstrmenu);
\r
2343 this.webService.removeAll();
\r
2344 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2346 webService.add( (JMenu) wsmenu.get(i));
\r
2351 this.webService.removeAll();
\r
2352 this.webService.add(this.webServiceNoServices);
\r
2354 // TODO: add in rediscovery function
\r
2355 // TODO: reduce code redundancy.
\r
2356 // TODO: group services by location as well as function.
\r