2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Softwarechang
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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21 import java.beans.*;
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26 import java.awt.datatransfer.*;
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27 import java.awt.event.*;
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28 import java.awt.print.*;
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29 import javax.swing.*;
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30 import javax.swing.event.*;
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32 import jalview.analysis.*;
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33 import jalview.datamodel.*;
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34 import jalview.io.*;
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35 import jalview.jbgui.*;
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36 import jalview.schemes.*;
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37 import jalview.ws.*;
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43 * @version $Revision$
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45 public class AlignFrame
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48 /** DOCUMENT ME!! */
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49 public static final int NEW_WINDOW_WIDTH = 700;
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51 /** DOCUMENT ME!! */
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52 public static final int NEW_WINDOW_HEIGHT = 500;
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53 final AlignmentPanel alignPanel;
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54 final AlignViewport viewport;
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56 /** DOCUMENT ME!! */
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57 public String currentFileFormat = null;
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58 Stack historyList = new Stack();
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59 Stack redoList = new Stack();
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60 private int treeCount = 0;
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63 * Creates a new AlignFrame object.
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65 * @param al DOCUMENT ME!
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67 public AlignFrame(AlignmentI al)
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69 viewport = new AlignViewport(al);
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71 alignPanel = new AlignmentPanel(this, viewport);
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72 alignPanel.annotationPanel.adjustPanelHeight();
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73 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
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74 annotationPanel.getPreferredSize());
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75 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
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76 getPreferredSize());
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77 alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
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79 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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81 addInternalFrameListener(new InternalFrameAdapter()
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83 public void internalFrameActivated(InternalFrameEvent evt)
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85 javax.swing.SwingUtilities.invokeLater(new Runnable()
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89 alignPanel.requestFocus();
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94 addServiceListeners();
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97 /* Set up intrinsic listeners for dynamically generated GUI bits. */
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98 private void addServiceListeners()
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100 final java.beans.PropertyChangeListener thisListener;
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101 // Do this once to get current state
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102 BuildWebServiceMenu();
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103 Desktop.discoverer.addPropertyChangeListener(
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104 thisListener = new java.beans.PropertyChangeListener()
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106 public void propertyChange(PropertyChangeEvent evt)
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108 // System.out.println("Discoverer property change.");
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109 if (evt.getPropertyName().equals("services"))
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111 // System.out.println("Rebuilding web service menu");
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112 BuildWebServiceMenu();
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116 addInternalFrameListener(new javax.swing.event.
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117 InternalFrameAdapter()
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119 public void internalFrameClosed(
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120 javax.swing.event.InternalFrameEvent evt)
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122 // System.out.println("deregistering discoverer listener");
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123 Desktop.discoverer.removePropertyChangeListener(thisListener);
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124 closeMenuItem_actionPerformed(null);
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134 * @param String DOCUMENT ME!
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137 public void parseGroupsFile(String file)
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141 BufferedReader in = new BufferedReader(new FileReader(file));
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142 SequenceI seq = null;
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143 String line, text, token;
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144 UserColourScheme ucs;
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145 int index, start, end;
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146 StringTokenizer st;
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148 while ( (line = in.readLine()) != null)
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150 st = new StringTokenizer(line, "\t");
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151 if (st.countTokens() != 6)
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153 System.out.println("Groups file " + file +
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154 " is invalid. Read help file.");
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158 while (st.hasMoreElements())
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160 text = st.nextToken();
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161 token = st.nextToken();
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162 if (!token.equals("ID_NOT_SPECIFIED"))
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164 index = viewport.alignment.findIndex(viewport.alignment.findName(
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170 index = Integer.parseInt(st.nextToken());
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173 start = Integer.parseInt(st.nextToken());
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174 end = Integer.parseInt(st.nextToken());
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175 ucs = new UserColourScheme(st.nextToken());
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177 seq = viewport.alignment.getSequenceAt(index);
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178 start = seq.findIndex(start) - 1;
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179 end = seq.findIndex(end) - 1;
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181 sg = new SequenceGroup(text, ucs, true, true, false, start, end);
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182 sg.addSequence(seq, true);
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184 viewport.alignment.addGroup(sg);
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189 catch (Exception ex)
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191 System.out.println("Error parsing groups file: " + ex);
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198 * @param e DOCUMENT ME!
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200 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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202 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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207 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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212 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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213 }, currentFileFormat);
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215 chooser.setAcceptAllFileFilterUsed(false);
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216 chooser.setFileView(new JalviewFileView());
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217 chooser.setDialogTitle("Save Alignment to file");
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218 chooser.setToolTipText("Save");
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220 int value = chooser.showSaveDialog(this);
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222 if (value == JalviewFileChooser.APPROVE_OPTION)
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224 currentFileFormat = chooser.getSelectedFormat();
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225 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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226 currentFileFormat);
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228 String choice = chooser.getSelectedFile().getPath();
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229 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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231 saveAlignment(choice, currentFileFormat);
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235 public boolean saveAlignment(String file, String format)
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237 if (format.equalsIgnoreCase("Jalview"))
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239 String shortName = title;
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241 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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243 shortName = shortName.substring(shortName.lastIndexOf(
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244 java.io.File.separatorChar) + 1);
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247 Jalview2XML.SaveAlignment(this, file, shortName);
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249 // USE Jalview2XML to save this file
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254 String output = FormatAdapter.formatSequences(format,
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255 viewport.getAlignment().
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257 if (output == null)
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264 java.io.PrintWriter out = new java.io.PrintWriter(
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265 new java.io.FileWriter(file));
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271 catch (Exception ex)
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273 ex.printStackTrace();
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282 * @param e DOCUMENT ME!
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284 protected void outputText_actionPerformed(ActionEvent e)
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286 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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287 Desktop.addInternalFrame(cap,
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288 "Alignment output - " + e.getActionCommand(), 600,
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290 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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291 viewport.getAlignment().
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298 * @param e DOCUMENT ME!
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300 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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302 new HTMLOutput(viewport);
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305 public void createImageMap(File file, String image)
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307 alignPanel.makePNGImageMap(file, image);
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313 * @param e DOCUMENT ME!
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315 public void createPNG(File f)
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317 alignPanel.makePNG(f);
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323 * @param e DOCUMENT ME!
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325 public void createEPS(File f)
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327 alignPanel.makeEPS(f);
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333 * @param e DOCUMENT ME!
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335 public void printMenuItem_actionPerformed(ActionEvent e)
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337 //Putting in a thread avoids Swing painting problems
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338 PrintThread thread = new PrintThread();
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345 * @param e DOCUMENT ME!
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347 public void closeMenuItem_actionPerformed(ActionEvent e)
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351 PaintRefresher.components.remove(viewport.alignment);
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352 this.setClosed(true);
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354 catch (Exception ex)
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362 void updateEditMenuBar()
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364 if (historyList.size() > 0)
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366 undoMenuItem.setEnabled(true);
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368 HistoryItem hi = (HistoryItem) historyList.peek();
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369 undoMenuItem.setText("Undo " + hi.getDescription());
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373 undoMenuItem.setEnabled(false);
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374 undoMenuItem.setText("Undo");
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377 if (redoList.size() > 0)
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379 redoMenuItem.setEnabled(true);
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381 HistoryItem hi = (HistoryItem) redoList.peek();
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382 redoMenuItem.setText("Redo " + hi.getDescription());
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386 redoMenuItem.setEnabled(false);
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387 redoMenuItem.setText("Redo");
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394 * @param hi DOCUMENT ME!
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396 public void addHistoryItem(HistoryItem hi)
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398 historyList.push(hi);
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399 updateEditMenuBar();
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405 * @param e DOCUMENT ME!
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407 protected void undoMenuItem_actionPerformed(ActionEvent e)
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409 HistoryItem hi = (HistoryItem) historyList.pop();
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410 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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411 HistoryItem.HIDE));
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412 restoreHistoryItem(hi);
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418 * @param e DOCUMENT ME!
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420 protected void redoMenuItem_actionPerformed(ActionEvent e)
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422 HistoryItem hi = (HistoryItem) redoList.pop();
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423 restoreHistoryItem(hi);
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424 updateEditMenuBar();
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425 viewport.updateConsensus();
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426 alignPanel.repaint();
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427 alignPanel.repaint();
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430 // used by undo and redo
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431 void restoreHistoryItem(HistoryItem hi)
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433 if (hi.getType() == HistoryItem.SORT)
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435 for (int i = 0; i < hi.getSequences().size(); i++)
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437 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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444 for (int i = 0; i < hi.getSequences().size(); i++)
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446 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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448 if (restore.getLength() == 0)
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450 restore.setSequence(hi.getHidden().elementAt(i).toString());
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451 viewport.alignment.getSequences().insertElementAt(restore,
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452 hi.getAlignIndex(i));
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456 restore.setSequence(hi.getHidden().elementAt(i).toString());
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460 if (hi.getType() == HistoryItem.PASTE)
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462 for (int i = viewport.alignment.getHeight() - 1;
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463 i > (hi.getSequences().size() - 1); i--)
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465 viewport.alignment.deleteSequence(i);
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470 updateEditMenuBar();
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472 viewport.updateConsensus();
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473 viewport.updateConservation();
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474 alignPanel.repaint();
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475 viewport.firePropertyChange("alignment", null,
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476 viewport.getAlignment().getSequences());
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482 * @param up DOCUMENT ME!
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484 public void moveSelectedSequences(boolean up)
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486 SequenceGroup sg = viewport.getSelectionGroup();
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495 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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497 SequenceI seq = viewport.alignment.getSequenceAt(i);
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499 if (!sg.sequences.contains(seq))
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504 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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506 if (sg.sequences.contains(temp))
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511 viewport.alignment.getSequences().setElementAt(temp, i);
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512 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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517 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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519 SequenceI seq = viewport.alignment.getSequenceAt(i);
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521 if (!sg.sequences.contains(seq))
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526 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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528 if (sg.sequences.contains(temp))
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533 viewport.alignment.getSequences().setElementAt(temp, i);
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534 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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538 alignPanel.repaint();
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544 * @param e DOCUMENT ME!
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546 protected void copy_actionPerformed(ActionEvent e)
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548 if (viewport.getSelectionGroup() == null)
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553 SequenceGroup sg = viewport.getSelectionGroup();
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555 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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556 StringBuffer buffer = new StringBuffer();
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558 Hashtable orderedSeqs = new Hashtable();
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560 for (int i = 0; i < sg.getSize(); i++)
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562 SequenceI seq = sg.getSequenceAt(i);
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563 int index = viewport.alignment.findIndex(seq);
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564 orderedSeqs.put(index + "", seq);
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567 int index = 0, startRes, endRes;
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570 for (int i = 0; i < sg.getSize(); i++)
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572 SequenceI seq = null;
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574 while (seq == null)
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576 if (orderedSeqs.containsKey(index + ""))
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578 seq = (SequenceI) orderedSeqs.get(index + "");
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589 //Returns residue following index if gap
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590 startRes = seq.findPosition(sg.getStartRes());
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593 //Need to find the residue preceeding index if gap
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596 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
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598 ch = seq.getCharAt(j);
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599 if (!jalview.util.Comparison.isGap( (ch)))
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607 endRes += seq.getStart() - 1;
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610 buffer.append(seq.getName() + "\t" +
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613 seq.getSequence(sg.getStartRes(),
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614 sg.getEndRes() + 1) + "\n");
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617 c.setContents(new StringSelection(buffer.toString()), null);
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623 * @param e DOCUMENT ME!
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625 protected void pasteNew_actionPerformed(ActionEvent e)
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633 * @param e DOCUMENT ME!
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635 protected void pasteThis_actionPerformed(ActionEvent e)
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637 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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638 HistoryItem.PASTE));
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645 * @param newAlignment DOCUMENT ME!
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647 void paste(boolean newAlignment)
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651 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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652 Transferable contents = c.getContents(this);
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654 if (contents == null)
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659 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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660 StringTokenizer st = new StringTokenizer(str);
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661 ArrayList seqs = new ArrayList();
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663 while (st.hasMoreElements())
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665 String name = st.nextToken();
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666 int start = Integer.parseInt(st.nextToken());
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667 int end = Integer.parseInt(st.nextToken());
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668 Sequence sequence = new Sequence(name, st.nextToken(), start,
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673 viewport.alignment.addSequence(sequence);
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677 seqs.add(sequence);
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683 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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684 seqs.toArray(newSeqs);
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686 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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687 String newtitle = new String("Copied sequences");
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689 if (title.startsWith("Copied sequences"))
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695 newtitle = newtitle.concat("- from " + title);
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698 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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699 NEW_WINDOW_HEIGHT);
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703 viewport.firePropertyChange("alignment", null,
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704 viewport.getAlignment().getSequences());
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705 viewport.setEndSeq(viewport.alignment.getHeight());
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706 viewport.alignment.getWidth();
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707 viewport.updateConservation();
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708 viewport.updateConsensus();
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709 alignPanel.repaint();
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712 catch (Exception ex)
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716 // could be anything being pasted in here
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722 * @param e DOCUMENT ME!
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724 protected void cut_actionPerformed(ActionEvent e)
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726 copy_actionPerformed(null);
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727 delete_actionPerformed(null);
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733 * @param e DOCUMENT ME!
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735 protected void delete_actionPerformed(ActionEvent e)
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737 boolean seqsdeleted = false;
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739 if (viewport.getSelectionGroup() == null)
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744 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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745 HistoryItem.HIDE));
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747 SequenceGroup sg = viewport.getSelectionGroup();
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748 boolean allSequences = false;
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749 if (sg.sequences.size() == viewport.alignment.getHeight())
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751 allSequences = true;
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754 for (int i = 0; i < sg.sequences.size(); i++)
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756 SequenceI seq = sg.getSequenceAt(i);
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757 int index = viewport.getAlignment().findIndex(seq);
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758 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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760 // If the cut affects all sequences, remove highlighted columns
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763 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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764 sg.getEndRes() + 1);
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767 if (seq.getSequence().length() < 1)
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769 seqsdeleted = true;
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770 viewport.getAlignment().deleteSequence(seq);
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774 viewport.getAlignment().getSequences().setElementAt(seq, index);
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778 viewport.setSelectionGroup(null);
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779 viewport.alignment.deleteGroup(sg);
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783 viewport.firePropertyChange("alignment", null,
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784 viewport.getAlignment().getSequences());
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787 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
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789 if (viewport.getAlignment().getHeight() < 1)
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793 this.setClosed(true);
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795 catch (Exception ex)
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800 viewport.updateConservation();
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801 viewport.updateConsensus();
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802 alignPanel.repaint();
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808 * @param e DOCUMENT ME!
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810 protected void deleteGroups_actionPerformed(ActionEvent e)
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812 viewport.alignment.deleteAllGroups();
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813 viewport.setSelectionGroup(null);
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814 alignPanel.repaint();
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820 * @param e DOCUMENT ME!
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822 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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824 SequenceGroup sg = new SequenceGroup();
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826 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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829 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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832 sg.setEndRes(viewport.alignment.getWidth() - 1);
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833 viewport.setSelectionGroup(sg);
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834 PaintRefresher.Refresh(null, viewport.alignment);
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840 * @param e DOCUMENT ME!
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842 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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844 viewport.setSelectionGroup(null);
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845 viewport.getColumnSelection().clear();
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846 viewport.setSelectionGroup(null);
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847 alignPanel.annotationPanel.activeRes = null;
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848 PaintRefresher.Refresh(null, viewport.alignment);
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854 * @param e DOCUMENT ME!
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856 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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858 SequenceGroup sg = viewport.getSelectionGroup();
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862 selectAllSequenceMenuItem_actionPerformed(null);
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867 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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870 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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873 PaintRefresher.Refresh(null, viewport.alignment);
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879 * @param e DOCUMENT ME!
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881 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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883 ColumnSelection colSel = viewport.getColumnSelection();
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885 if (colSel.size() > 0)
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887 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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888 HistoryItem.HIDE));
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890 int min = colSel.getMin();
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891 viewport.getAlignment().trimLeft(min);
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892 colSel.compensateForEdit(0, min);
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894 if (viewport.getSelectionGroup() != null)
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896 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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899 Vector groups = viewport.alignment.getGroups();
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901 for (int i = 0; i < groups.size(); i++)
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903 SequenceGroup sg = (SequenceGroup) groups.get(i);
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905 if (!sg.adjustForRemoveLeft(min))
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907 viewport.alignment.deleteGroup(sg);
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911 alignPanel.repaint();
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918 * @param e DOCUMENT ME!
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920 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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922 ColumnSelection colSel = viewport.getColumnSelection();
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924 if (colSel.size() > 0)
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926 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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927 HistoryItem.HIDE));
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929 int max = colSel.getMax();
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930 viewport.getAlignment().trimRight(max);
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932 if (viewport.getSelectionGroup() != null)
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934 viewport.getSelectionGroup().adjustForRemoveRight(max);
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937 Vector groups = viewport.alignment.getGroups();
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939 for (int i = 0; i < groups.size(); i++)
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941 SequenceGroup sg = (SequenceGroup) groups.get(i);
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943 if (!sg.adjustForRemoveRight(max))
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945 viewport.alignment.deleteGroup(sg);
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949 alignPanel.repaint();
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956 * @param e DOCUMENT ME!
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958 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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960 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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961 viewport.alignment, HistoryItem.HIDE));
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963 //This is to maintain viewport position on first residue
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964 //of first sequence
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965 SequenceI seq = viewport.alignment.getSequenceAt(0);
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966 int startRes = seq.findPosition(viewport.startRes);
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968 viewport.getAlignment().removeGaps();
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970 viewport.setStartRes(seq.findIndex(startRes)-1);
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972 resetAllClustalSchemes();
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973 viewport.updateConservation();
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974 viewport.updateConsensus();
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975 alignPanel.repaint();
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981 * @param e DOCUMENT ME!
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983 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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985 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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986 HistoryItem.HIDE));
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988 //This is to maintain viewport position on first residue
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989 //of first sequence
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990 SequenceI seq = viewport.alignment.getSequenceAt(0);
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991 int startRes = seq.findPosition(viewport.startRes);
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997 Vector seqs = null;
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1000 int end = viewport.alignment.getWidth();
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1002 if (viewport.getSelectionGroup() != null
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1003 && viewport.getSelectionGroup().sequences != null
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1004 && viewport.getSelectionGroup().sequences.size() > 0)
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1006 seqs = viewport.getSelectionGroup().sequences;
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1007 start = viewport.getSelectionGroup().getStartRes();
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1008 end = viewport.getSelectionGroup().getEndRes();
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1012 seqs = viewport.alignment.getSequences();
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1015 for (int i = 0; i < seqs.size(); i++)
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1017 current = (SequenceI) seqs.elementAt(i);
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1018 jSize = current.getLength();
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1024 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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1026 current.deleteCharAt(j);
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1032 while (j < end && j < jSize);
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1035 viewport.setStartRes(seq.findIndex(startRes)-1);
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1037 resetAllClustalSchemes();
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1039 viewport.updateConservation();
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1040 viewport.updateConsensus();
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1041 alignPanel.repaint();
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1044 void resetAllClustalSchemes()
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1046 if(viewport.getGlobalColourScheme()!=null
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1047 && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
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1049 ((ClustalxColourScheme)viewport.getGlobalColourScheme()).
\r
1050 resetClustalX(viewport.alignment.getSequences(),
\r
1051 viewport.alignment.getWidth());
\r
1054 int s, sSize = viewport.alignment.getGroups().size();
\r
1055 for(s=0; s<sSize; s++)
\r
1057 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1058 if(sg.cs instanceof ClustalxColourScheme)
\r
1060 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1068 * @param e DOCUMENT ME!
\r
1070 public void padGapsMenuitem_actionPerformed(ActionEvent e)
\r
1072 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
1073 HistoryItem.HIDE));
\r
1075 SequenceI current;
\r
1076 int Width = viewport.getAlignment().getWidth();
\r
1078 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1081 current = viewport.getAlignment().getSequenceAt(i);
\r
1083 if (current.getLength() < Width)
\r
1085 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1089 viewport.updateConservation();
\r
1090 viewport.updateConsensus();
\r
1091 alignPanel.repaint();
\r
1097 * @param e DOCUMENT ME!
\r
1099 public void findMenuItem_actionPerformed(ActionEvent e)
\r
1101 JInternalFrame frame = new JInternalFrame();
\r
1102 Finder finder = new Finder(viewport, alignPanel, frame);
\r
1103 frame.setContentPane(finder);
\r
1104 Desktop.addInternalFrame(frame, "Find", 340, 110);
\r
1105 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1111 * @param e DOCUMENT ME!
\r
1113 public void font_actionPerformed(ActionEvent e)
\r
1115 FontChooser fc = new FontChooser(alignPanel);
\r
1121 * @param e DOCUMENT ME!
\r
1123 protected void fullSeqId_actionPerformed(ActionEvent e)
\r
1125 viewport.setShowFullId(fullSeqId.isSelected());
\r
1127 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
\r
1128 alignPanel.repaint();
\r
1134 * @param e DOCUMENT ME!
\r
1136 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
1138 viewport.setColourText(colourTextMenuItem.isSelected());
\r
1139 alignPanel.repaint();
\r
1145 * @param e DOCUMENT ME!
\r
1147 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
1149 viewport.setWrapAlignment(wrapMenuItem.isSelected());
\r
1150 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
\r
1151 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1152 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1153 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1154 alignPanel.repaint();
\r
1160 * @param e DOCUMENT ME!
\r
1162 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1164 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1165 alignPanel.repaint();
\r
1171 * @param e DOCUMENT ME!
\r
1173 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1175 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1176 alignPanel.repaint();
\r
1182 * @param e DOCUMENT ME!
\r
1184 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1186 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1187 alignPanel.repaint();
\r
1193 * @param e DOCUMENT ME!
\r
1195 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1197 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1198 alignPanel.repaint();
\r
1204 * @param e DOCUMENT ME!
\r
1206 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1208 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1209 alignPanel.repaint();
\r
1215 * @param e DOCUMENT ME!
\r
1217 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1219 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1220 alignPanel.repaint();
\r
1226 * @param evt DOCUMENT ME!
\r
1228 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1230 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1232 if (viewport.showSequenceFeatures &&
\r
1233 ! ( (Alignment) viewport.alignment).featuresAdded)
\r
1235 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
\r
1238 ( (Alignment) viewport.alignment).featuresAdded = true;
\r
1241 alignPanel.repaint();
\r
1247 * @param e DOCUMENT ME!
\r
1249 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1251 if (annotationPanelMenuItem.isSelected() &&
\r
1252 viewport.getWrapAlignment())
\r
1254 annotationPanelMenuItem.setSelected(false);
\r
1259 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1260 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1266 * @param e DOCUMENT ME!
\r
1268 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1270 if (alignPanel.overviewPanel != null)
\r
1275 JInternalFrame frame = new JInternalFrame();
\r
1276 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1277 frame.setContentPane(overview);
\r
1278 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1279 frame.getWidth(), frame.getHeight());
\r
1281 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1282 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1284 public void internalFrameClosed(
\r
1285 javax.swing.event.InternalFrameEvent evt)
\r
1287 alignPanel.setOverviewPanel(null);
\r
1292 alignPanel.setOverviewPanel(overview);
\r
1298 * @param e DOCUMENT ME!
\r
1300 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1302 changeColour(null);
\r
1308 * @param e DOCUMENT ME!
\r
1310 public void clustalColour_actionPerformed(ActionEvent e)
\r
1312 changeColour(new ClustalxColourScheme(
\r
1313 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1319 * @param e DOCUMENT ME!
\r
1321 public void zappoColour_actionPerformed(ActionEvent e)
\r
1323 changeColour(new ZappoColourScheme());
\r
1329 * @param e DOCUMENT ME!
\r
1331 public void taylorColour_actionPerformed(ActionEvent e)
\r
1333 changeColour(new TaylorColourScheme());
\r
1339 * @param e DOCUMENT ME!
\r
1341 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1343 changeColour(new HydrophobicColourScheme());
\r
1349 * @param e DOCUMENT ME!
\r
1351 public void helixColour_actionPerformed(ActionEvent e)
\r
1353 changeColour(new HelixColourScheme());
\r
1359 * @param e DOCUMENT ME!
\r
1361 public void strandColour_actionPerformed(ActionEvent e)
\r
1363 changeColour(new StrandColourScheme());
\r
1369 * @param e DOCUMENT ME!
\r
1371 public void turnColour_actionPerformed(ActionEvent e)
\r
1373 changeColour(new TurnColourScheme());
\r
1379 * @param e DOCUMENT ME!
\r
1381 public void buriedColour_actionPerformed(ActionEvent e)
\r
1383 changeColour(new BuriedColourScheme());
\r
1389 * @param e DOCUMENT ME!
\r
1391 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1393 changeColour(new NucleotideColourScheme());
\r
1399 * @param e DOCUMENT ME!
\r
1401 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1403 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1409 * @param cs DOCUMENT ME!
\r
1411 void changeColour(ColourSchemeI cs)
\r
1413 int threshold = 0;
\r
1417 if (viewport.getAbovePIDThreshold())
\r
1419 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1422 cs.setThreshold(threshold,
\r
1423 viewport.getIgnoreGapsConsensus());
\r
1425 viewport.setGlobalColourScheme(cs);
\r
1429 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1432 if (viewport.getConservationSelected())
\r
1435 Alignment al = (Alignment) viewport.alignment;
\r
1436 Conservation c = new Conservation("All",
\r
1437 ResidueProperties.propHash, 3,
\r
1438 al.getSequences(), 0,
\r
1439 al.getWidth() - 1);
\r
1442 c.verdict(false, viewport.ConsPercGaps);
\r
1444 cs.setConservation(c);
\r
1446 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1451 cs.setConservation(null);
\r
1454 cs.setConsensus(viewport.vconsensus);
\r
1457 viewport.setGlobalColourScheme(cs);
\r
1459 if (viewport.getColourAppliesToAllGroups())
\r
1461 Vector groups = viewport.alignment.getGroups();
\r
1463 for (int i = 0; i < groups.size(); i++)
\r
1465 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1473 if (cs instanceof ClustalxColourScheme)
\r
1475 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1477 else if (cs instanceof UserColourScheme)
\r
1479 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1485 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1487 catch (Exception ex)
\r
1492 if (viewport.getAbovePIDThreshold()
\r
1493 || cs instanceof PIDColourScheme
\r
1494 || cs instanceof Blosum62ColourScheme)
\r
1496 sg.cs.setThreshold(threshold,
\r
1497 viewport.getIgnoreGapsConsensus());
\r
1499 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1503 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1506 if (viewport.getConservationSelected())
\r
1508 Conservation c = new Conservation("Group",
\r
1509 ResidueProperties.propHash, 3,
\r
1511 viewport.alignment.getWidth() - 1);
\r
1513 c.verdict(false, viewport.ConsPercGaps);
\r
1514 sg.cs.setConservation(c);
\r
1517 sg.cs.setConservation(null);
\r
1521 if (alignPanel.getOverviewPanel() != null)
\r
1523 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1526 alignPanel.repaint();
\r
1532 * @param e DOCUMENT ME!
\r
1534 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1536 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1538 SliderPanel.setPIDSliderSource(alignPanel,
\r
1539 viewport.getGlobalColourScheme(),
\r
1541 SliderPanel.showPIDSlider();
\r
1548 * @param e DOCUMENT ME!
\r
1550 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1552 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1554 SliderPanel.setConservationSlider(alignPanel,
\r
1555 viewport.globalColourScheme,
\r
1557 SliderPanel.showConservationSlider();
\r
1564 * @param e DOCUMENT ME!
\r
1566 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1568 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1570 viewport.setAbovePIDThreshold(false);
\r
1571 abovePIDThreshold.setSelected(false);
\r
1573 changeColour(viewport.getGlobalColourScheme());
\r
1575 modifyConservation_actionPerformed(null);
\r
1581 * @param e DOCUMENT ME!
\r
1583 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1585 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1587 conservationMenuItem.setSelected(false);
\r
1588 viewport.setConservationSelected(false);
\r
1590 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1592 changeColour(viewport.getGlobalColourScheme());
\r
1594 modifyPID_actionPerformed(null);
\r
1600 * @param e DOCUMENT ME!
\r
1602 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1604 if (e.getActionCommand().equals("User Defined..."))
\r
1606 new UserDefinedColours(alignPanel, null);
\r
1610 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
1611 getUserColourSchemes().get(e.getActionCommand());
\r
1613 changeColour(udc);
\r
1617 public void updateUserColourMenu()
\r
1620 Component[] menuItems = colourMenu.getMenuComponents();
\r
1621 int i, iSize = menuItems.length;
\r
1622 for (i = 0; i < iSize; i++)
\r
1624 if (menuItems[i].getName() != null &&
\r
1625 menuItems[i].getName().equals("USER_DEFINED"))
\r
1627 colourMenu.remove(menuItems[i]);
\r
1631 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
1633 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1634 getUserColourSchemes().keys();
\r
1636 while (userColours.hasMoreElements())
\r
1638 final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1639 nextElement().toString());
\r
1640 radioItem.setName("USER_DEFINED");
\r
1641 radioItem.addMouseListener(new MouseAdapter()
\r
1643 public void mousePressed(MouseEvent evt)
\r
1645 if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
\r
1647 radioItem.removeActionListener(radioItem.getActionListeners()[0]);
\r
1649 int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
\r
1650 "Remove from default list?",
\r
1651 "Remove user defined colour",
\r
1652 JOptionPane.YES_NO_OPTION);
\r
1653 if(option == JOptionPane.YES_OPTION)
\r
1655 jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
\r
1656 colourMenu.remove(radioItem);
\r
1659 radioItem.addActionListener(new ActionListener()
\r
1661 public void actionPerformed(ActionEvent evt)
\r
1663 userDefinedColour_actionPerformed(evt);
\r
1669 radioItem.addActionListener(new ActionListener()
\r
1671 public void actionPerformed(ActionEvent evt)
\r
1673 userDefinedColour_actionPerformed(evt);
\r
1677 colourMenu.insert(radioItem, 15);
\r
1678 colours.add(radioItem);
\r
1686 * @param e DOCUMENT ME!
\r
1688 public void PIDColour_actionPerformed(ActionEvent e)
\r
1690 changeColour(new PIDColourScheme());
\r
1696 * @param e DOCUMENT ME!
\r
1698 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1700 changeColour(new Blosum62ColourScheme());
\r
1706 * @param e DOCUMENT ME!
\r
1708 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1710 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1711 HistoryItem.SORT));
\r
1712 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1713 viewport.getAlignment().getSequenceAt(0));
\r
1714 alignPanel.repaint();
\r
1720 * @param e DOCUMENT ME!
\r
1722 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1724 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1725 HistoryItem.SORT));
\r
1726 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1727 alignPanel.repaint();
\r
1733 * @param e DOCUMENT ME!
\r
1735 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1737 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1738 HistoryItem.SORT));
\r
1740 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1741 alignPanel.repaint();
\r
1747 * @param e DOCUMENT ME!
\r
1749 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1751 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1752 JInternalFrame frame = new JInternalFrame();
\r
1753 frame.setContentPane(sp);
\r
1754 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1761 * @param e DOCUMENT ME!
\r
1763 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1765 if ( (viewport.getSelectionGroup() == null) ||
\r
1766 (viewport.getSelectionGroup().getSize() < 2))
\r
1768 JOptionPane.showInternalMessageDialog(this,
\r
1769 "You must select at least 2 sequences.",
\r
1770 "Invalid Selection",
\r
1771 JOptionPane.WARNING_MESSAGE);
\r
1775 JInternalFrame frame = new JInternalFrame();
\r
1776 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1777 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1784 * @param e DOCUMENT ME!
\r
1786 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1788 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1789 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1790 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1791 (viewport.getAlignment().getHeight() < 4))
\r
1793 JOptionPane.showInternalMessageDialog(this,
\r
1794 "Principal component analysis must take\n" +
\r
1795 "at least 4 input sequences.",
\r
1796 "Sequence selection insufficient",
\r
1797 JOptionPane.WARNING_MESSAGE);
\r
1804 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1805 JInternalFrame frame = new JInternalFrame();
\r
1806 frame.setContentPane(pcaPanel);
\r
1807 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1810 catch (java.lang.OutOfMemoryError ex)
\r
1812 JOptionPane.showInternalMessageDialog(this,
\r
1813 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1815 JOptionPane.WARNING_MESSAGE);
\r
1822 * @param e DOCUMENT ME!
\r
1824 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1826 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1832 * @param e DOCUMENT ME!
\r
1834 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1836 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1842 * @param e DOCUMENT ME!
\r
1844 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1846 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1852 * @param e DOCUMENT ME!
\r
1854 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1856 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1862 * @param type DOCUMENT ME!
\r
1863 * @param pwType DOCUMENT ME!
\r
1864 * @param title DOCUMENT ME!
\r
1866 void NewTreePanel(String type, String pwType, String title)
\r
1868 final TreePanel tp;
\r
1870 if ( (viewport.getSelectionGroup() != null) &&
\r
1871 (viewport.getSelectionGroup().getSize() > 3))
\r
1874 SequenceGroup sg = viewport.getSelectionGroup();
\r
1876 /* Decide if the selection is a column region */
\r
1877 while (s < sg.sequences.size())
\r
1879 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1882 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1883 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1884 "Try using the Pad function in the edit menu,\n" +
\r
1885 "or one of the multiple sequence alignment web services.",
\r
1886 "Sequences in selection are not aligned",
\r
1887 JOptionPane.WARNING_MESSAGE);
\r
1893 title = title + " on region";
\r
1894 tp = new TreePanel(viewport,
\r
1895 viewport.getSelectionGroup().sequences, type, pwType,
\r
1896 sg.getStartRes(), sg.getEndRes());
\r
1900 //are the sequences aligned?
\r
1901 if (!viewport.alignment.isAligned())
\r
1903 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1904 "The sequences must be aligned before creating a tree.\n" +
\r
1905 "Try using the Pad function in the edit menu,\n" +
\r
1906 "or one of the multiple sequence alignment web services.",
\r
1907 "Sequences not aligned",
\r
1908 JOptionPane.WARNING_MESSAGE);
\r
1913 tp = new TreePanel(viewport,
\r
1914 viewport.getAlignment().getSequences(), type, pwType,
\r
1916 viewport.alignment.getWidth());
\r
1919 addTreeMenuItem(tp, title);
\r
1920 viewport.setCurrentTree(tp.getTree());
\r
1922 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1928 * @param title DOCUMENT ME!
\r
1929 * @param order DOCUMENT ME!
\r
1931 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1933 final JMenuItem item = new JMenuItem("by " + title);
\r
1935 item.addActionListener(new java.awt.event.ActionListener()
\r
1937 public void actionPerformed(ActionEvent e)
\r
1939 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1940 HistoryItem.SORT));
\r
1942 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1943 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1944 alignPanel.repaint();
\r
1950 * Maintain the Order by->Displayed Tree menu.
\r
1951 * Creates a new menu item for a TreePanel with an appropriate
\r
1952 * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added
\r
1953 * to remove the menu item when the treePanel is closed, and adjust
\r
1954 * the tree leaf to sequence mapping when the alignment is modified.
\r
1955 * @param treePanel Displayed tree window.
\r
1956 * @param title SortBy menu item title.
\r
1958 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1960 final JMenuItem item = new JMenuItem(title);
\r
1964 if (treeCount == 1)
\r
1966 sort.add(sortByTreeMenu);
\r
1969 sortByTreeMenu.add(item);
\r
1970 item.addActionListener(new java.awt.event.ActionListener()
\r
1972 public void actionPerformed(ActionEvent e)
\r
1974 addHistoryItem(new HistoryItem("Tree Sort",
\r
1975 viewport.alignment, HistoryItem.SORT));
\r
1976 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1977 treePanel.getTree());
\r
1978 alignPanel.repaint();
\r
1982 treePanel.addInternalFrameListener(new javax.swing.event.
\r
1983 InternalFrameAdapter()
\r
1985 public void internalFrameClosed(
\r
1986 javax.swing.event.InternalFrameEvent evt)
\r
1989 sortByTreeMenu.remove(item);
\r
1991 if (treeCount == 0)
\r
1993 sort.remove(sortByTreeMenu);
\r
1998 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
2000 public void propertyChange(PropertyChangeEvent evt)
\r
2002 if (evt.getPropertyName().equals("alignment"))
\r
2004 treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
2005 treePanel.repaint();
\r
2012 * Work out whether the whole set of sequences
\r
2013 * or just the selected set will be submitted for multiple alignment.
\r
2016 private SequenceI[] gatherSequencesForAlignment()
\r
2018 // Now, check we have enough sequences
\r
2019 SequenceI[] msa = null;
\r
2021 if ( (viewport.getSelectionGroup() != null) &&
\r
2022 (viewport.getSelectionGroup().getSize() > 1))
\r
2024 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2025 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2027 msa = new SequenceI[sz = seqs.getSize()];
\r
2029 for (int i = 0; i < sz; i++)
\r
2031 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2036 Vector seqs = viewport.getAlignment().getSequences();
\r
2038 if (seqs.size() > 1)
\r
2040 msa = new SequenceI[seqs.size()];
\r
2042 for (int i = 0; i < seqs.size(); i++)
\r
2044 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2052 * Decides what is submitted to a secondary structure prediction service,
\r
2053 * the currently selected sequence, or the currently selected alignment
\r
2054 * (where the first sequence in the set is the one that the prediction
\r
2057 SequenceI[] gatherSeqOrMsaForSecStrPrediction()
\r
2059 SequenceI seq = null;
\r
2060 SequenceI[] msa = null;
\r
2062 if ( (viewport.getSelectionGroup() != null) &&
\r
2063 (viewport.getSelectionGroup().getSize() > 0))
\r
2065 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2066 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2068 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2070 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2075 msa = new SequenceI[sz = seqs.getSize()];
\r
2077 for (int i = 0; i < sz; i++)
\r
2079 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2085 Vector seqs = viewport.getAlignment().getSequences();
\r
2087 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2089 seq = (SequenceI) seqs.elementAt(0);
\r
2093 msa = new SequenceI[seqs.size()];
\r
2095 for (int i = 0; i < seqs.size(); i++)
\r
2097 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2109 return new SequenceI[]
\r
2119 * @param e DOCUMENT ME!
\r
2121 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2123 // Pick the tree file
\r
2124 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
2126 "LAST_DIRECTORY"));
\r
2127 chooser.setFileView(new JalviewFileView());
\r
2128 chooser.setDialogTitle("Select a newick-like tree file");
\r
2129 chooser.setToolTipText("Load a tree file");
\r
2131 int value = chooser.showOpenDialog(null);
\r
2133 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2135 String choice = chooser.getSelectedFile().getPath();
\r
2136 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2140 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2142 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2144 catch (Exception ex)
\r
2146 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2147 "Problem reading tree file",
\r
2149 JOptionPane.WARNING_MESSAGE);
\r
2150 ex.printStackTrace();
\r
2156 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2158 return ShowNewickTree(nf,title,600,500,4,5);
\r
2163 * @param nf DOCUMENT ME!
\r
2164 * @param title DOCUMENT ME!
\r
2166 * @return DOCUMENT ME!
\r
2168 public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
2170 TreePanel tp = null;
\r
2176 if (nf.getTree() != null)
\r
2178 tp = new TreePanel(viewport,
\r
2179 viewport.getAlignment().getSequences(), nf,
\r
2186 tp.setLocation(x,y);
\r
2189 Desktop.addInternalFrame(tp, title, w, h);
\r
2190 addTreeMenuItem(tp, title);
\r
2193 catch (Exception ex)
\r
2195 ex.printStackTrace();
\r
2206 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2207 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2208 printJob.setPrintable(alignPanel, pf);
\r
2210 if (printJob.printDialog())
\r
2216 catch (Exception PrintException)
\r
2218 PrintException.printStackTrace();
\r
2225 * Generates menu items and listener event actions for web service clients
\r
2228 public void BuildWebServiceMenu()
\r
2230 if ( (Desktop.discoverer.services != null)
\r
2231 && (Desktop.discoverer.services.size() > 0))
\r
2233 Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
\r
2234 Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
\r
2235 Vector wsmenu = new Vector();
\r
2236 if (msaws != null)
\r
2238 // Add any Multiple Sequence Alignment Services
\r
2239 final JMenu msawsmenu = new JMenu("Alignment");
\r
2240 for (int i = 0, j = msaws.size(); i < j; i++)
\r
2242 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
\r
2244 final JMenuItem method = new JMenuItem(sh.getName());
\r
2245 method.addActionListener(new ActionListener()
\r
2247 public void actionPerformed(ActionEvent e)
\r
2249 SequenceI[] msa = gatherSequencesForAlignment();
\r
2250 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2256 msawsmenu.add(method);
\r
2257 // Deal with services that we know accept partial alignments.
\r
2258 if (sh.getName().indexOf("lustal") > -1)
\r
2260 // We know that ClustalWS can accept partial alignments for refinement.
\r
2261 final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
\r
2262 methodR.addActionListener(new ActionListener()
\r
2264 public void actionPerformed(ActionEvent e)
\r
2266 SequenceI[] msa = gatherSequencesForAlignment();
\r
2267 MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
\r
2273 msawsmenu.add(methodR);
\r
2277 wsmenu.add(msawsmenu);
\r
2279 if (secstrpr != null)
\r
2281 // Add any secondary structure prediction services
\r
2282 final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
\r
2283 for (int i = 0, j = secstrpr.size(); i < j; i++)
\r
2285 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
\r
2287 final JMenuItem method = new JMenuItem(sh.getName());
\r
2288 method.addActionListener(new ActionListener()
\r
2290 public void actionPerformed(ActionEvent e)
\r
2292 SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();
\r
2293 if (msa.length == 1)
\r
2295 // Single Sequence prediction
\r
2296 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2301 if (msa.length > 1)
\r
2303 // Single Sequence prediction
\r
2304 jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
\r
2310 secstrmenu.add(method);
\r
2312 wsmenu.add(secstrmenu);
\r
2314 this.webService.removeAll();
\r
2315 for (int i = 0, j = wsmenu.size(); i < j; i++)
\r
2317 webService.add( (JMenu) wsmenu.get(i));
\r
2322 this.webService.removeAll();
\r
2323 this.webService.add(this.webServiceNoServices);
\r
2325 // TODO: add in rediscovery function
\r
2326 // TODO: reduce code redundancy.
\r
2327 // TODO: group services by location as well as function.
\r