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 Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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22 import jalview.schemes.*;
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23 import jalview.datamodel.*;
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24 import jalview.analysis.*;
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25 import jalview.io.*;
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27 import java.awt.event.*;
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29 import java.io.InputStreamReader;
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30 import java.io.BufferedReader;
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31 import java.net.URL;
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34 public class AlignFrame extends Frame
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36 final AlignmentPanel alignPanel;
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37 public final AlignViewport viewport;
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38 int NEW_WINDOW_WIDTH = 700;
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39 int NEW_WINDOW_HEIGHT = 500;
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40 jalview.bin.JalviewLite applet;
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43 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
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47 }catch(Exception ex)
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49 ex.printStackTrace();
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52 this.applet = applet;
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53 viewport = new AlignViewport(al, applet);
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54 alignPanel = new AlignmentPanel(this, viewport);
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56 alignPanel.validate();
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60 String param = applet.getParameter("sortBy");
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63 if (param.equalsIgnoreCase("Id"))
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64 sortIDMenuItem_actionPerformed(null);
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65 else if (param.equalsIgnoreCase("Pairwise Identity"))
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66 sortPairwiseMenuItem_actionPerformed(null);
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69 param = applet.getParameter("wrap");
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72 if (param.equalsIgnoreCase("true"))
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74 wrapMenuItem.setState(true);
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75 wrapMenuItem_actionPerformed(null);
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81 param = applet.getParameter("windowWidth");
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84 int width = Integer.parseInt(param);
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85 NEW_WINDOW_WIDTH = width;
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87 param = applet.getParameter("windowHeight");
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90 int height = Integer.parseInt(param);
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91 NEW_WINDOW_HEIGHT = height;
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94 catch (Exception ex)
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99 MyKeyAdapter keyAdapter = new MyKeyAdapter();
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100 //Some JVMS send keyevents to Top frame or lowest panel,
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101 //Havent worked out why yet. So add to both this frame and seqCanvas for now
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102 this.addKeyListener(keyAdapter);
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103 alignPanel.seqPanel.seqCanvas.addKeyListener(keyAdapter);
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104 alignPanel.idPanel.idCanvas.addKeyListener(keyAdapter);
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106 this.addWindowListener(new WindowAdapter()
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108 public void windowClosing(WindowEvent e)
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110 closeMenuItem_actionPerformed(null);
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114 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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116 public void propertyChange(java.beans.PropertyChangeEvent evt)
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118 if (evt.getPropertyName().equals("alignment"))
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120 alignmentChanged();
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125 jalview.bin.JalviewLite.addFrame(this, title,
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127 NEW_WINDOW_HEIGHT);
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130 public AlignViewport getAlignViewport()
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135 public SeqCanvas getSeqcanvas()
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137 return alignPanel.seqPanel.seqCanvas;
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144 * @param String DOCUMENT ME!
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147 public void parseFeaturesFile(String file)
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151 URL url = new URL(file);
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153 BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
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154 SequenceI seq = null;
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155 String line, type, desc, token;
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157 int index, start, end;
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158 StringTokenizer st;
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159 SequenceFeature sf;
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160 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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162 while ( (line = in.readLine()) != null)
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165 st = new StringTokenizer(line, "\t");
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166 if (st.countTokens() == 2)
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168 type = st.nextToken();
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169 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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170 fr.setColour(type, ucs.findColour("A"));
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174 while (st.hasMoreElements())
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176 desc = st.nextToken();
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177 token = st.nextToken();
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178 if (!token.equals("ID_NOT_SPECIFIED"))
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180 index = viewport.alignment.findIndex(viewport.alignment.findName(
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186 index = Integer.parseInt(st.nextToken());
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189 start = Integer.parseInt(st.nextToken());
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190 end = Integer.parseInt(st.nextToken());
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192 seq = viewport.alignment.getSequenceAt(index);
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193 start = seq.findIndex(start) - 1;
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194 end = seq.findIndex(end) - 1;
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196 type = st.nextToken();
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198 if(fr.getColour(type)==null)
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200 // Probably the old style groups file
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201 UserColourScheme ucs = new UserColourScheme(type);
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202 fr.setColour(type, ucs.findColour("A"));
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205 sf = new SequenceFeature(type, desc, "", start, end);
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207 seq.addSequenceFeature(sf);
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211 viewport.showSequenceFeatures = true;
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213 alignPanel.repaint();
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216 catch (Exception ex)
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218 System.out.println("Error parsing groups file: " + ex);
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223 class MyKeyAdapter extends KeyAdapter
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226 public void keyPressed(KeyEvent evt)
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228 switch (evt.getKeyCode())
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230 case 27: // escape key
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231 deselectAllSequenceMenuItem_actionPerformed(null);
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233 case KeyEvent.VK_X:
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234 if (evt.isControlDown() || evt.isMetaDown())
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236 cut_actionPerformed(null);
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239 case KeyEvent.VK_C:
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240 if (evt.isControlDown() || evt.isMetaDown())
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242 copy_actionPerformed(null);
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245 case KeyEvent.VK_V:
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246 if (evt.isControlDown() || evt.isMetaDown())
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251 case KeyEvent.VK_A:
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252 if (evt.isControlDown() || evt.isMetaDown())
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254 selectAllSequenceMenuItem_actionPerformed(null);
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257 case KeyEvent.VK_DOWN:
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258 moveSelectedSequences(false);
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260 case KeyEvent.VK_UP:
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261 moveSelectedSequences(true);
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263 case KeyEvent.VK_F:
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264 if (evt.isControlDown())
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266 findMenuItem_actionPerformed(null);
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269 case KeyEvent.VK_BACK_SPACE:
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270 case KeyEvent.VK_DELETE:
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271 cut_actionPerformed(null);
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279 public void inputText_actionPerformed(ActionEvent e)
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281 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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282 Frame frame = new Frame();
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284 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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287 protected void outputText_actionPerformed(ActionEvent e)
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289 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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290 Frame frame = new Frame();
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292 jalview.bin.JalviewLite.addFrame(frame,
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293 "Alignment output - " + e.getActionCommand(),
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295 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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296 viewport.getAlignment().getSequences(),
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297 viewport.showJVSuffix));
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300 public void closeMenuItem_actionPerformed(ActionEvent e)
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302 PaintRefresher.components.remove(viewport.alignment);
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303 if(PaintRefresher.components.size()==0 && applet==null)
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307 Stack historyList = new Stack();
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308 Stack redoList = new Stack();
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310 void updateEditMenuBar()
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312 if (historyList.size() > 0)
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314 undoMenuItem.setEnabled(true);
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315 HistoryItem hi = (HistoryItem) historyList.peek();
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316 undoMenuItem.setLabel("Undo " + hi.getDescription());
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320 undoMenuItem.setEnabled(false);
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321 undoMenuItem.setLabel("Undo");
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324 if (redoList.size() > 0)
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326 redoMenuItem.setEnabled(true);
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327 HistoryItem hi = (HistoryItem) redoList.peek();
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328 redoMenuItem.setLabel("Redo " + hi.getDescription());
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332 redoMenuItem.setEnabled(false);
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333 redoMenuItem.setLabel("Redo");
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337 public void addHistoryItem(HistoryItem hi)
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339 historyList.push(hi);
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340 updateEditMenuBar();
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343 protected void undoMenuItem_actionPerformed(ActionEvent e)
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345 HistoryItem hi = (HistoryItem) historyList.pop();
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346 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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347 HistoryItem.HIDE));
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348 restoreHistoryItem(hi);
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349 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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352 protected void redoMenuItem_actionPerformed(ActionEvent e)
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354 HistoryItem hi = (HistoryItem) redoList.pop();
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355 restoreHistoryItem(hi);
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356 updateEditMenuBar();
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357 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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360 // used by undo and redo
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361 void restoreHistoryItem(HistoryItem hi)
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363 if (hi.getType() == HistoryItem.SORT)
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365 for (int i = 0; i < hi.getSequences().size(); i++)
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367 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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373 for (int i = 0; i < hi.getSequences().size(); i++)
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375 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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376 if (restore.getLength() == 0)
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378 // log.System.out.println(hi.getHidden().elementAt(i));
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379 restore.setSequence(hi.getHidden().elementAt(i).toString());
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380 viewport.alignment.getSequences().insertElementAt(
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382 hi.getAlignIndex(i));
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386 restore.setSequence(hi.getHidden().elementAt(i).toString());
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389 if (hi.getType() == HistoryItem.PASTE)
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391 for (int i = viewport.alignment.getHeight() - 1;
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392 i > hi.getSequences().size() - 1; i--)
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394 viewport.alignment.deleteSequence(i);
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399 updateEditMenuBar();
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401 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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404 public void moveSelectedSequences(boolean up)
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406 SequenceGroup sg = viewport.getSelectionGroup();
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414 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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416 SequenceI seq = viewport.alignment.getSequenceAt(i);
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417 if (!sg.sequences.contains(seq))
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422 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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423 if (sg.sequences.contains(temp))
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428 viewport.alignment.getSequences().setElementAt(temp, i);
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429 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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434 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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436 SequenceI seq = viewport.alignment.getSequenceAt(i);
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437 if (!sg.sequences.contains(seq))
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442 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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443 if (sg.sequences.contains(temp))
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448 viewport.alignment.getSequences().setElementAt(temp, i);
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449 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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453 alignPanel.repaint();
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456 StringBuffer copiedSequences;
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457 protected void copy_actionPerformed(ActionEvent e)
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459 if (viewport.getSelectionGroup() == null)
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464 SequenceGroup sg = viewport.getSelectionGroup();
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465 copiedSequences = new StringBuffer();
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466 Hashtable orderedSeqs = new Hashtable();
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467 for (int i = 0; i < sg.getSize(); i++)
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469 SequenceI seq = sg.getSequenceAt(i);
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470 int index = viewport.alignment.findIndex(seq);
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471 orderedSeqs.put(index + "", seq);
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474 int index = 0, startRes, endRes;
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477 for (int i = 0; i < sg.getSize(); i++)
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479 SequenceI seq = null;
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481 while (seq == null)
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483 if (orderedSeqs.containsKey(index + ""))
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485 seq = (SequenceI) orderedSeqs.get(index + "");
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497 //Returns residue following index if gap
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498 startRes = seq.findPosition(sg.getStartRes());
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501 //Need to find the residue preceeding index if gap
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504 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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506 ch = seq.getCharAt(j);
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507 if (!jalview.util.Comparison.isGap( (ch)))
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515 endRes += seq.getStart() -1;
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518 copiedSequences.append(seq.getName() + "\t" +
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521 seq.getSequence(sg.getStartRes(),
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522 sg.getEndRes() + 1) + "\n");
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527 protected void pasteNew_actionPerformed(ActionEvent e)
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532 protected void pasteThis_actionPerformed(ActionEvent e)
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534 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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535 HistoryItem.PASTE));
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539 void paste(boolean newAlignment)
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543 if (copiedSequences == null)
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548 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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549 Vector seqs = new Vector();
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550 while (st.hasMoreElements())
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552 String name = st.nextToken();
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553 int start = Integer.parseInt(st.nextToken());
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554 int end = Integer.parseInt(st.nextToken());
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555 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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559 viewport.alignment.addSequence(sequence);
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563 seqs.addElement(sequence);
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569 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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570 for (int i = 0; i < seqs.size(); i++)
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572 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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575 String newtitle = new String("Copied sequences");
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576 if (getTitle().startsWith("Copied sequences"))
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578 newtitle = getTitle();
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582 newtitle = newtitle.concat("- from " + getTitle());
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584 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
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586 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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587 NEW_WINDOW_HEIGHT);
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591 viewport.setEndSeq(viewport.alignment.getHeight());
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592 viewport.alignment.getWidth();
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593 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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597 catch (Exception ex)
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598 {} // could be anything being pasted in here
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602 protected void cut_actionPerformed(ActionEvent e)
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604 copy_actionPerformed(null);
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605 delete_actionPerformed(null);
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608 protected void delete_actionPerformed(ActionEvent e)
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610 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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611 HistoryItem.HIDE));
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612 if (viewport.getSelectionGroup() == null)
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618 SequenceGroup sg = viewport.getSelectionGroup();
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619 boolean allSequences = false;
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620 if(sg.sequences.size()==viewport.alignment.getHeight())
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621 allSequences = true;
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623 for (int i = 0; i < sg.sequences.size(); i++)
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625 SequenceI seq = sg.getSequenceAt(i);
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626 int index = viewport.getAlignment().findIndex(seq);
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627 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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629 // If the cut affects all sequences, remove highlighted columns
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632 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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633 sg.getEndRes() + 1);
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637 if (seq.getSequence().length() < 1)
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639 viewport.getAlignment().deleteSequence(seq);
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643 viewport.getAlignment().getSequences().setElementAt(seq, index);
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647 viewport.setSelectionGroup(null);
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648 viewport.alignment.deleteGroup(sg);
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649 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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650 if (viewport.getAlignment().getHeight() < 1)
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654 this.setVisible(false);
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656 catch (Exception ex)
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659 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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663 protected void deleteGroups_actionPerformed(ActionEvent e)
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665 viewport.alignment.deleteAllGroups();
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666 viewport.setSelectionGroup(null);
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668 alignPanel.repaint();
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671 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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673 SequenceGroup sg = new SequenceGroup();
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674 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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676 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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678 sg.setEndRes(viewport.alignment.getWidth()-1);
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679 viewport.setSelectionGroup(sg);
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680 alignPanel.repaint();
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681 PaintRefresher.Refresh(null, viewport.alignment);
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684 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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686 viewport.setSelectionGroup(null);
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687 viewport.getColumnSelection().clear();
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688 viewport.setSelectionGroup(null);
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689 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
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690 alignPanel.repaint();
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691 PaintRefresher.Refresh(null, viewport.alignment);
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694 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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696 SequenceGroup sg = viewport.getSelectionGroup();
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697 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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699 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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702 PaintRefresher.Refresh(null, viewport.alignment);
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705 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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707 ColumnSelection colSel = viewport.getColumnSelection();
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708 if (colSel.size() > 0)
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710 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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711 HistoryItem.HIDE));
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712 int min = colSel.getMin();
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713 viewport.getAlignment().trimLeft(min);
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714 colSel.compensateForEdit(0, min);
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716 if (viewport.getSelectionGroup() != null)
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718 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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721 Vector groups = viewport.alignment.getGroups();
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722 for (int i = 0; i < groups.size(); i++)
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724 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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725 if (!sg.adjustForRemoveLeft(min))
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727 viewport.alignment.deleteGroup(sg);
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730 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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734 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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736 ColumnSelection colSel = viewport.getColumnSelection();
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737 if (colSel.size() > 0)
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739 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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740 HistoryItem.HIDE));
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741 int max = colSel.getMax();
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742 viewport.getAlignment().trimRight(max);
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743 if (viewport.getSelectionGroup() != null)
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745 viewport.getSelectionGroup().adjustForRemoveRight(max);
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748 Vector groups = viewport.alignment.getGroups();
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749 for (int i = 0; i < groups.size(); i++)
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751 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
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752 if (!sg.adjustForRemoveRight(max))
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754 viewport.alignment.deleteGroup(sg);
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757 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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762 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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764 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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765 viewport.alignment,
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766 HistoryItem.HIDE));
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768 //This is to maintain viewport position on first residue
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769 //of first sequence
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770 SequenceI seq = viewport.alignment.getSequenceAt(0);
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771 int startRes = seq.findPosition(viewport.startRes);
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773 viewport.getAlignment().removeGaps();
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775 viewport.setStartRes(seq.findIndex(startRes)-1);
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777 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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780 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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782 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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783 HistoryItem.HIDE));
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785 //This is to maintain viewport position on first residue
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786 //of first sequence
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787 SequenceI seq = viewport.alignment.getSequenceAt(0);
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788 int startRes = seq.findPosition(viewport.startRes);
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795 int start=0, end = viewport.alignment.getWidth();
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797 if (viewport.getSelectionGroup() != null
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798 && viewport.getSelectionGroup().sequences != null
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799 && viewport.getSelectionGroup().sequences.size()>0)
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801 seqs = viewport.getSelectionGroup().sequences;
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802 start = viewport.getSelectionGroup().getStartRes();
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803 end = viewport.getSelectionGroup().getEndRes()+1;
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806 seqs = viewport.alignment.getSequences();
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808 for (int i = 0; i < seqs.size(); i++)
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810 current = (SequenceI) seqs.elementAt(i);
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811 jSize = current.getLength();
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813 // Removing a range is much quicker than removing gaps
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814 // one by one for long sequences
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816 int rangeStart=-1, rangeEnd=-1;
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820 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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837 current.deleteChars(rangeStart, rangeEnd);
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838 j-=rangeEnd-rangeStart;
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839 jSize-=rangeEnd-rangeStart;
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847 while (j < end && j < jSize);
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850 current.deleteChars(rangeStart, rangeEnd);
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853 viewport.setStartRes(seq.findIndex(startRes)-1);
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854 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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857 public void alignmentChanged()
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859 viewport.updateConsensus();
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860 viewport.updateConservation ();
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861 resetAllColourSchemes();
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862 if(alignPanel.overviewPanel!=null)
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863 alignPanel.overviewPanel.updateOverviewImage();
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864 alignPanel.repaint();
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867 void resetAllColourSchemes()
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869 ColourSchemeI cs = viewport.globalColourScheme;
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872 if (cs instanceof ClustalxColourScheme)
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874 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
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875 resetClustalX(viewport.alignment.getSequences(),
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876 viewport.alignment.getWidth());
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879 cs.setConsensus(viewport.vconsensus);
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880 if (cs.conservationApplied())
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882 Alignment al = (Alignment) viewport.alignment;
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883 Conservation c = new Conservation("All",
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884 ResidueProperties.propHash, 3,
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885 al.getSequences(), 0,
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886 al.getWidth() - 1);
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888 c.verdict(false, viewport.ConsPercGaps);
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890 cs.setConservation(c);
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894 int s, sSize = viewport.alignment.getGroups().size();
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895 for(s=0; s<sSize; s++)
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897 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
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898 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
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900 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
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902 sg.recalcConservation();
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908 public void findMenuItem_actionPerformed(ActionEvent e)
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910 new Finder(alignPanel);
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913 public void font_actionPerformed(ActionEvent e)
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915 new FontChooser(alignPanel);
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919 public void seqLimits_itemStateChanged(ItemEvent e)
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921 viewport.setShowJVSuffix(seqLimits.getState());
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922 alignPanel.fontChanged();
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923 alignPanel.repaint();
\r
927 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
\r
929 viewport.setColourText(colourTextMenuItem.getState());
\r
930 alignPanel.repaint();
\r
933 protected void wrapMenuItem_actionPerformed(ActionEvent e)
\r
935 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
936 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
937 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
938 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
939 scaleRight.setEnabled(wrapMenuItem.getState());
\r
940 alignPanel.repaint();
\r
943 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
945 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
946 alignPanel.repaint();
\r
949 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
951 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
952 alignPanel.repaint();
\r
955 protected void scaleRight_actionPerformed(ActionEvent e)
\r
957 viewport.setScaleRightWrapped(scaleRight.getState());
\r
958 alignPanel.repaint();
\r
961 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
963 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
964 alignPanel.repaint();
\r
967 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
969 viewport.setShowText(viewTextMenuItem.getState());
\r
970 alignPanel.repaint();
\r
973 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
975 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
976 alignPanel.repaint();
\r
979 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
981 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
982 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
985 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
987 if (alignPanel.overviewPanel != null)
\r
992 Frame frame = new Frame();
\r
993 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
994 frame.add(overview);
\r
995 // +50 must allow for applet frame window
\r
996 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
997 overview.preferredSize().width,
\r
998 overview.preferredSize().height + 50);
\r
1001 frame.addWindowListener(new WindowAdapter()
\r
1003 public void windowClosing(WindowEvent e)
\r
1005 alignPanel.setOverviewPanel(null);
\r
1009 alignPanel.setOverviewPanel(overview);
\r
1013 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1015 changeColour(null);
\r
1018 public void clustalColour_actionPerformed(ActionEvent e)
\r
1020 abovePIDThreshold.setState(false);
\r
1021 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1022 viewport.alignment.getWidth()));
\r
1025 public void zappoColour_actionPerformed(ActionEvent e)
\r
1027 changeColour(new ZappoColourScheme());
\r
1030 public void taylorColour_actionPerformed(ActionEvent e)
\r
1032 changeColour(new TaylorColourScheme());
\r
1035 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1037 changeColour(new HydrophobicColourScheme());
\r
1040 public void helixColour_actionPerformed(ActionEvent e)
\r
1042 changeColour(new HelixColourScheme());
\r
1045 public void strandColour_actionPerformed(ActionEvent e)
\r
1047 changeColour(new StrandColourScheme());
\r
1050 public void turnColour_actionPerformed(ActionEvent e)
\r
1052 changeColour(new TurnColourScheme());
\r
1055 public void buriedColour_actionPerformed(ActionEvent e)
\r
1057 changeColour(new BuriedColourScheme());
\r
1060 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1062 changeColour(new NucleotideColourScheme());
\r
1065 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1067 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1070 void changeColour(ColourSchemeI cs)
\r
1072 int threshold = 0;
\r
1076 if (viewport.getAbovePIDThreshold())
\r
1078 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1080 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1082 viewport.setGlobalColourScheme(cs);
\r
1086 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1089 if (viewport.getConservationSelected())
\r
1092 Alignment al = (Alignment) viewport.alignment;
\r
1093 Conservation c = new Conservation("All",
\r
1094 ResidueProperties.propHash, 3,
\r
1095 al.getSequences(), 0,
\r
1096 al.getWidth() - 1);
\r
1099 c.verdict(false, viewport.ConsPercGaps);
\r
1101 cs.setConservation(c);
\r
1103 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1109 cs.setConservation(null);
\r
1112 cs.setConsensus(viewport.vconsensus);
\r
1115 viewport.setGlobalColourScheme(cs);
\r
1117 if (viewport.getColourAppliesToAllGroups())
\r
1119 Vector groups = viewport.alignment.getGroups();
\r
1120 for (int i = 0; i < groups.size(); i++)
\r
1122 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1129 if (cs instanceof ClustalxColourScheme)
\r
1131 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1137 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1139 catch (Exception ex)
\r
1141 ex.printStackTrace();
\r
1146 if (viewport.getAbovePIDThreshold()
\r
1147 || cs instanceof PIDColourScheme
\r
1148 || cs instanceof Blosum62ColourScheme)
\r
1150 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1151 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1154 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1156 if (viewport.getConservationSelected())
\r
1158 Conservation c = new Conservation("Group",
\r
1159 ResidueProperties.propHash, 3,
\r
1161 viewport.alignment.getWidth() - 1);
\r
1163 c.verdict(false, viewport.ConsPercGaps);
\r
1164 sg.cs.setConservation(c);
\r
1168 sg.cs.setConservation(null);
\r
1169 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1176 if (alignPanel.getOverviewPanel() != null)
\r
1178 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1181 alignPanel.repaint();
\r
1186 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1188 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1190 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1192 SliderPanel.showPIDSlider();
\r
1196 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1198 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1200 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1202 SliderPanel.showConservationSlider();
\r
1206 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1208 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1210 viewport.setAbovePIDThreshold(false);
\r
1211 abovePIDThreshold.setState(false);
\r
1213 changeColour(viewport.getGlobalColourScheme());
\r
1215 modifyConservation_actionPerformed(null);
\r
1218 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1220 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1222 conservationMenuItem.setState(false);
\r
1223 viewport.setConservationSelected(false);
\r
1225 changeColour(viewport.getGlobalColourScheme());
\r
1227 modifyPID_actionPerformed(null);
\r
1230 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1232 new UserDefinedColours(alignPanel, null);
\r
1235 public void PIDColour_actionPerformed(ActionEvent e)
\r
1237 changeColour(new PIDColourScheme());
\r
1240 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1242 changeColour(new Blosum62ColourScheme());
\r
1245 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1247 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1248 HistoryItem.SORT));
\r
1249 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1250 viewport.getAlignment().getSequenceAt(0));
\r
1251 alignPanel.repaint();
\r
1254 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1256 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1257 HistoryItem.SORT));
\r
1258 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1259 alignPanel.repaint();
\r
1262 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1264 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1265 HistoryItem.SORT));
\r
1266 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1267 alignPanel.repaint();
\r
1271 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1273 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1274 Frame frame = new Frame();
\r
1276 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1281 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1283 if (viewport.getSelectionGroup().getSize() > 1)
\r
1285 Frame frame = new Frame();
\r
1286 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1287 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1291 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1293 //are the sequences aligned?
\r
1294 if (!viewport.alignment.isAligned())
\r
1296 SequenceI current;
\r
1297 int Width = viewport.getAlignment().getWidth();
\r
1299 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1302 current = viewport.getAlignment().getSequenceAt(i);
\r
1304 if (current.getLength() < Width)
\r
1306 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1309 alignPanel.repaint();
\r
1312 if ( (viewport.getSelectionGroup() != null &&
\r
1313 viewport.getSelectionGroup().getSize() < 4 &&
\r
1314 viewport.getSelectionGroup().getSize() > 0)
\r
1315 || viewport.getAlignment().getHeight() < 4)
\r
1322 new PCAPanel(viewport);
\r
1324 catch (java.lang.OutOfMemoryError ex)
\r
1330 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1332 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1335 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1337 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1340 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1342 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1345 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1347 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1350 void NewTreePanel(String type, String pwType, String title)
\r
1352 //are the sequences aligned?
\r
1353 if (!viewport.alignment.isAligned())
\r
1355 SequenceI current;
\r
1356 int Width = viewport.getAlignment().getWidth();
\r
1358 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1361 current = viewport.getAlignment().getSequenceAt(i);
\r
1363 if (current.getLength() < Width)
\r
1365 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1368 alignPanel.repaint();
\r
1372 final TreePanel tp;
\r
1373 if (viewport.getSelectionGroup() != null &&
\r
1374 viewport.getSelectionGroup().getSize() > 3)
\r
1376 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1378 0, viewport.alignment.getWidth());
\r
1382 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1383 type, pwType, 0, viewport.alignment.getWidth());
\r
1386 addTreeMenuItem(tp, title);
\r
1388 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1391 public void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1393 final MenuItem item = new MenuItem(title);
\r
1394 sortByTreeMenu.add(item);
\r
1395 item.addActionListener(new java.awt.event.ActionListener()
\r
1397 public void actionPerformed(ActionEvent e)
\r
1399 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1400 HistoryItem.SORT));
\r
1401 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1402 alignPanel.repaint();
\r
1406 treePanel.addWindowListener(new WindowAdapter()
\r
1408 public void windowClosing(WindowEvent e)
\r
1410 sortByTreeMenu.remove(item);
\r
1415 protected void documentation_actionPerformed(ActionEvent e)
\r
1417 showURL("http://www.jalview.org/help.html");
\r
1420 protected void about_actionPerformed(ActionEvent e)
\r
1423 class AboutPanel extends Canvas
\r
1426 public AboutPanel(String version)
\r
1427 { this.version = version; }
\r
1429 public void paint(Graphics g)
\r
1431 g.setColor(Color.white);
\r
1432 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1433 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1434 FontMetrics fm = g.getFontMetrics();
\r
1435 int fh = fm.getHeight();
\r
1437 g.setColor(Color.black);
\r
1438 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1439 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1440 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1441 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1443 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1446 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1448 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1449 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1451 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1455 String version = "test";
\r
1456 java.net.URL url = getClass().getResource("/.build_properties");
\r
1461 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1462 url.openStream()));
\r
1464 while ( (line = reader.readLine()) != null)
\r
1466 if (line.indexOf("VERSION") > -1)
\r
1468 version = line.substring(line.indexOf("=") + 1);
\r
1472 catch (Exception ex)
\r
1474 ex.printStackTrace();
\r
1479 Frame frame = new Frame();
\r
1480 frame.add(new AboutPanel(version));
\r
1481 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1486 * Displays the given URL in a new browser window
\r
1488 * @param url URL to display in browser window.
\r
1489 * <br>New window will be named "HELP_WINDOW"
\r
1491 public void showURL(String url)
\r
1493 showURL(url, "HELP");
\r
1496 public void showURL(String url, String target)
\r
1498 if (applet == null)
\r
1500 System.out.println("Not running as applet - no browser available.");
\r
1506 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1509 catch (Exception ex)
\r
1511 ex.printStackTrace();
\r
1517 //////////////////////////////////////////////////////////////////////////////////
\r
1518 //JBuilder Graphics here
\r
1520 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1521 protected Menu fileMenu = new Menu();
\r
1522 protected MenuItem closeMenuItem = new MenuItem();
\r
1523 protected Menu editMenu = new Menu();
\r
1524 protected Menu viewMenu = new Menu();
\r
1525 protected Menu colourMenu = new Menu();
\r
1526 protected Menu calculateMenu = new Menu();
\r
1527 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
\r
1528 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
\r
1529 protected MenuItem invertSequenceMenuItem = new MenuItem();
\r
1530 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1531 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1532 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1533 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1534 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1535 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1536 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1537 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1538 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1539 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1540 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1541 protected MenuItem PCAMenuItem = new MenuItem();
\r
1542 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1543 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1544 BorderLayout borderLayout1 = new BorderLayout();
\r
1545 public Label statusBar = new Label();
\r
1546 protected Menu outputTextboxMenu = new Menu();
\r
1547 protected MenuItem clustalColour = new MenuItem();
\r
1548 protected MenuItem zappoColour = new MenuItem();
\r
1549 protected MenuItem taylorColour = new MenuItem();
\r
1550 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1551 protected MenuItem helixColour = new MenuItem();
\r
1552 protected MenuItem strandColour = new MenuItem();
\r
1553 protected MenuItem turnColour = new MenuItem();
\r
1554 protected MenuItem buriedColour = new MenuItem();
\r
1555 protected MenuItem userDefinedColour = new MenuItem();
\r
1556 protected MenuItem PIDColour = new MenuItem();
\r
1557 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1558 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1559 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1560 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1561 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1562 MenuItem overviewMenuItem = new MenuItem();
\r
1563 protected MenuItem undoMenuItem = new MenuItem();
\r
1564 protected MenuItem redoMenuItem = new MenuItem();
\r
1565 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1566 MenuItem noColourmenuItem = new MenuItem();
\r
1567 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1568 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1569 MenuItem findMenuItem = new MenuItem();
\r
1570 Menu searchMenu = new Menu();
\r
1571 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1572 protected MenuItem nucleotideColour = new MenuItem();
\r
1573 MenuItem deleteGroups = new MenuItem();
\r
1574 MenuItem delete = new MenuItem();
\r
1575 MenuItem copy = new MenuItem();
\r
1576 MenuItem cut = new MenuItem();
\r
1577 Menu Menu1 = new Menu();
\r
1578 MenuItem pasteNew = new MenuItem();
\r
1579 MenuItem pasteThis = new MenuItem();
\r
1580 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1581 protected MenuItem font = new MenuItem();
\r
1582 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1583 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1584 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1585 MenuItem modifyPID = new MenuItem();
\r
1586 MenuItem modifyConservation = new MenuItem();
\r
1587 protected Menu sortByTreeMenu = new Menu();
\r
1588 Menu sort = new Menu();
\r
1589 Menu calculate = new Menu();
\r
1590 MenuItem inputText = new MenuItem();
\r
1591 Menu helpMenu = new Menu();
\r
1592 MenuItem documentation = new MenuItem();
\r
1593 MenuItem about = new MenuItem();
\r
1594 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1596 private void jbInit() throws Exception {
\r
1598 setMenuBar(alignFrameMenuBar);
\r
1602 // dynamically fill save as menu with available formats
\r
1603 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1606 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1609 item.addActionListener(new java.awt.event.ActionListener()
\r
1611 public void actionPerformed(ActionEvent e)
\r
1613 outputText_actionPerformed(e);
\r
1617 outputTextboxMenu.add(item);
\r
1621 fileMenu.setLabel("File");
\r
1622 closeMenuItem.setLabel("Close");
\r
1623 closeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1624 public void actionPerformed(ActionEvent e) {
\r
1625 closeMenuItem_actionPerformed(e);
\r
1628 editMenu.setLabel("Edit");
\r
1629 viewMenu.setLabel("View");
\r
1630 colourMenu.setLabel("Colour");
\r
1631 calculateMenu.setLabel("Calculate");
\r
1632 selectAllSequenceMenuItem.setLabel("Select all");
\r
1633 selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1634 public void actionPerformed(ActionEvent e) {
\r
1635 selectAllSequenceMenuItem_actionPerformed(e);
\r
1638 deselectAllSequenceMenuItem.setLabel("Deselect All");
\r
1639 deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1640 public void actionPerformed(ActionEvent e) {
\r
1641 deselectAllSequenceMenuItem_actionPerformed(e);
\r
1644 invertSequenceMenuItem.setLabel("Invert Selection");
\r
1645 invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1646 public void actionPerformed(ActionEvent e) {
\r
1647 invertSequenceMenuItem_actionPerformed(e);
\r
1650 remove2LeftMenuItem.setLabel("Remove Left");
\r
1651 remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1652 public void actionPerformed(ActionEvent e) {
\r
1653 remove2LeftMenuItem_actionPerformed(e);
\r
1656 remove2RightMenuItem.setLabel("Remove Right");
\r
1657 remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1658 public void actionPerformed(ActionEvent e) {
\r
1659 remove2RightMenuItem_actionPerformed(e);
\r
1662 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1663 removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1664 public void actionPerformed(ActionEvent e) {
\r
1665 removeGappedColumnMenuItem_actionPerformed(e);
\r
1668 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1669 removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1670 public void actionPerformed(ActionEvent e) {
\r
1671 removeAllGapsMenuItem_actionPerformed(e);
\r
1674 viewBoxesMenuItem.setLabel("Boxes");
\r
1675 viewBoxesMenuItem.setState(true);
\r
1676 viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1677 public void itemStateChanged(ItemEvent e) {
\r
1678 viewBoxesMenuItem_actionPerformed(null);
\r
1681 viewTextMenuItem.setLabel("Text");
\r
1682 viewTextMenuItem.setState(true);
\r
1683 viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1684 public void itemStateChanged(ItemEvent e) {
\r
1685 viewTextMenuItem_actionPerformed(null);
\r
1688 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1689 sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1690 public void actionPerformed(ActionEvent e) {
\r
1691 sortPairwiseMenuItem_actionPerformed(e);
\r
1694 sortIDMenuItem.setLabel("by ID");
\r
1695 sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1696 public void actionPerformed(ActionEvent e) {
\r
1697 sortIDMenuItem_actionPerformed(e);
\r
1700 sortGroupMenuItem.setLabel("by Group");
\r
1701 sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1702 public void actionPerformed(ActionEvent e) {
\r
1703 sortGroupMenuItem_actionPerformed(e);
\r
1706 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1707 removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1708 public void actionPerformed(ActionEvent e) {
\r
1709 removeRedundancyMenuItem_actionPerformed(e);
\r
1712 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1713 pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1714 public void actionPerformed(ActionEvent e) {
\r
1715 pairwiseAlignmentMenuItem_actionPerformed(e);
\r
1718 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1719 PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1720 public void actionPerformed(ActionEvent e) {
\r
1721 PCAMenuItem_actionPerformed(e);
\r
1724 averageDistanceTreeMenuItem.setLabel(
\r
1725 "Average Distance Using % Identity");
\r
1726 averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1727 public void actionPerformed(ActionEvent e) {
\r
1728 averageDistanceTreeMenuItem_actionPerformed(e);
\r
1731 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1732 neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1733 public void actionPerformed(ActionEvent e) {
\r
1734 neighbourTreeMenuItem_actionPerformed(e);
\r
1737 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1738 statusBar.setBackground(Color.white);
\r
1739 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1740 statusBar.setText("Status bar");
\r
1741 outputTextboxMenu.setLabel("Output to Textbox");
\r
1742 clustalColour.setLabel("Clustalx");
\r
1744 clustalColour.addActionListener(new java.awt.event.ActionListener() {
\r
1745 public void actionPerformed(ActionEvent e) {
\r
1746 clustalColour_actionPerformed(e);
\r
1749 zappoColour.setLabel("Zappo");
\r
1750 zappoColour.addActionListener(new java.awt.event.ActionListener() {
\r
1751 public void actionPerformed(ActionEvent e) {
\r
1752 zappoColour_actionPerformed(e);
\r
1755 taylorColour.setLabel("Taylor");
\r
1756 taylorColour.addActionListener(new java.awt.event.ActionListener() {
\r
1757 public void actionPerformed(ActionEvent e) {
\r
1758 taylorColour_actionPerformed(e);
\r
1761 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1762 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {
\r
1763 public void actionPerformed(ActionEvent e) {
\r
1764 hydrophobicityColour_actionPerformed(e);
\r
1767 helixColour.setLabel("Helix Propensity");
\r
1768 helixColour.addActionListener(new java.awt.event.ActionListener() {
\r
1769 public void actionPerformed(ActionEvent e) {
\r
1770 helixColour_actionPerformed(e);
\r
1773 strandColour.setLabel("Strand Propensity");
\r
1774 strandColour.addActionListener(new java.awt.event.ActionListener() {
\r
1775 public void actionPerformed(ActionEvent e) {
\r
1776 strandColour_actionPerformed(e);
\r
1779 turnColour.setLabel("Turn Propensity");
\r
1780 turnColour.addActionListener(new java.awt.event.ActionListener() {
\r
1781 public void actionPerformed(ActionEvent e) {
\r
1782 turnColour_actionPerformed(e);
\r
1785 buriedColour.setLabel("Buried Index");
\r
1786 buriedColour.addActionListener(new java.awt.event.ActionListener() {
\r
1787 public void actionPerformed(ActionEvent e) {
\r
1788 buriedColour_actionPerformed(e);
\r
1791 userDefinedColour.setLabel("User Defined...");
\r
1792 userDefinedColour.addActionListener(new java.awt.event.ActionListener() {
\r
1793 public void actionPerformed(ActionEvent e) {
\r
1794 userDefinedColour_actionPerformed(e);
\r
1797 PIDColour.setLabel("Percentage Identity");
\r
1798 PIDColour.addActionListener(new java.awt.event.ActionListener() {
\r
1799 public void actionPerformed(ActionEvent e) {
\r
1800 PIDColour_actionPerformed(e);
\r
1803 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1804 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {
\r
1805 public void actionPerformed(ActionEvent e) {
\r
1806 BLOSUM62Colour_actionPerformed(e);
\r
1809 avDistanceTreeBlosumMenuItem.setLabel(
\r
1810 "Average Distance Using BLOSUM62");
\r
1811 avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1812 public void actionPerformed(ActionEvent e) {
\r
1813 avTreeBlosumMenuItem_actionPerformed(e);
\r
1816 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1817 njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1818 public void actionPerformed(ActionEvent e) {
\r
1819 njTreeBlosumMenuItem_actionPerformed(e);
\r
1822 annotationPanelMenuItem.setActionCommand("");
\r
1823 annotationPanelMenuItem.setState(true);
\r
1824 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1825 annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1826 public void itemStateChanged(ItemEvent e) {
\r
1827 annotationPanelMenuItem_actionPerformed(null);
\r
1830 colourTextMenuItem.setLabel("Colour Text");
\r
1831 colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1832 public void itemStateChanged(ItemEvent e) {
\r
1833 colourTextMenuItem_actionPerformed(null);
\r
1836 overviewMenuItem.setLabel("Overview Window");
\r
1837 overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1838 public void actionPerformed(ActionEvent e) {
\r
1839 overviewMenuItem_actionPerformed(e);
\r
1842 undoMenuItem.setEnabled(false);
\r
1843 undoMenuItem.setLabel("Undo");
\r
1844 undoMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1845 public void actionPerformed(ActionEvent e) {
\r
1846 undoMenuItem_actionPerformed(e);
\r
1849 redoMenuItem.setEnabled(false);
\r
1850 redoMenuItem.setLabel("Redo");
\r
1851 redoMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1852 public void actionPerformed(ActionEvent e) {
\r
1853 redoMenuItem_actionPerformed(e);
\r
1856 conservationMenuItem.setLabel("by Conservation");
\r
1857 conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1858 public void itemStateChanged(ItemEvent e) {
\r
1859 conservationMenuItem_actionPerformed(null);
\r
1862 noColourmenuItem.setLabel("None");
\r
1863 noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1864 public void actionPerformed(ActionEvent e) {
\r
1865 noColourmenuItem_actionPerformed(e);
\r
1868 wrapMenuItem.setLabel("Wrap");
\r
1869 wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1870 public void itemStateChanged(ItemEvent e) {
\r
1871 wrapMenuItem_actionPerformed(null);
\r
1874 renderGapsMenuItem.setLabel("Show Gaps");
\r
1875 renderGapsMenuItem.setState(true);
\r
1876 renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {
\r
1877 public void itemStateChanged(ItemEvent e) {
\r
1878 renderGapsMenuItem_actionPerformed(null);
\r
1881 findMenuItem.setLabel("Find...");
\r
1882 findMenuItem.addActionListener(new java.awt.event.ActionListener() {
\r
1883 public void actionPerformed(ActionEvent e) {
\r
1884 findMenuItem_actionPerformed(e);
\r
1887 searchMenu.setLabel("Search");
\r
1889 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1890 abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {
\r
1891 public void itemStateChanged(ItemEvent e) {
\r
1892 abovePIDThreshold_actionPerformed(null);
\r
1895 nucleotideColour.setLabel("Nucleotide");
\r
1896 nucleotideColour.addActionListener(new java.awt.event.ActionListener() {
\r
1897 public void actionPerformed(ActionEvent e) {
\r
1898 nucleotideColour_actionPerformed(e);
\r
1901 deleteGroups.setLabel("Undefine Groups");
\r
1902 deleteGroups.addActionListener(new java.awt.event.ActionListener() {
\r
1903 public void actionPerformed(ActionEvent e) {
\r
1904 deleteGroups_actionPerformed(e);
\r
1907 copy.setLabel("Copy");
\r
1908 copy.addActionListener(new java.awt.event.ActionListener() {
\r
1909 public void actionPerformed(ActionEvent e) {
\r
1910 copy_actionPerformed(e);
\r
1913 cut.setLabel("Cut");
\r
1914 cut.addActionListener(new java.awt.event.ActionListener() {
\r
1915 public void actionPerformed(ActionEvent e) {
\r
1916 cut_actionPerformed(e);
\r
1919 delete.setLabel("Delete");
\r
1920 delete.addActionListener(new java.awt.event.ActionListener() {
\r
1921 public void actionPerformed(ActionEvent e) {
\r
1922 delete_actionPerformed(e);
\r
1925 Menu1.setLabel("Paste");
\r
1926 pasteNew.setLabel("To New Alignment");
\r
1927 pasteNew.addActionListener(new java.awt.event.ActionListener() {
\r
1928 public void actionPerformed(ActionEvent e) {
\r
1929 pasteNew_actionPerformed(e);
\r
1932 pasteThis.setLabel("Add To This Alignment");
\r
1933 pasteThis.addActionListener(new java.awt.event.ActionListener() {
\r
1934 public void actionPerformed(ActionEvent e) {
\r
1935 pasteThis_actionPerformed(e);
\r
1938 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1939 applyToAllGroups.setState(true);
\r
1940 applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {
\r
1941 public void itemStateChanged(ItemEvent e) {
\r
1942 applyToAllGroups_actionPerformed(null);
\r
1945 font.setLabel("Font...");
\r
1946 font.addActionListener(new java.awt.event.ActionListener() {
\r
1947 public void actionPerformed(ActionEvent e) {
\r
1948 font_actionPerformed(e);
\r
1951 scaleAbove.setLabel("Scale Above");
\r
1952 scaleAbove.setState(true);
\r
1953 scaleAbove.addItemListener(new java.awt.event.ItemListener() {
\r
1954 public void itemStateChanged(ItemEvent e) {
\r
1955 scaleAbove_actionPerformed(null);
\r
1958 scaleLeft.setEnabled(false);
\r
1959 scaleLeft.setState(true);
\r
1960 scaleLeft.setLabel("Scale Left");
\r
1961 scaleLeft.addItemListener(new java.awt.event.ItemListener() {
\r
1962 public void itemStateChanged(ItemEvent e) {
\r
1963 scaleLeft_actionPerformed(null);
\r
1966 scaleRight.setEnabled(false);
\r
1967 scaleRight.setState(true);
\r
1968 scaleRight.setLabel("Scale Right");
\r
1969 scaleRight.addItemListener(new java.awt.event.ItemListener() {
\r
1970 public void itemStateChanged(ItemEvent e) {
\r
1971 scaleRight_actionPerformed(null);
\r
1974 modifyPID.setLabel("Modify Identity Threshold...");
\r
1975 modifyPID.addActionListener(new java.awt.event.ActionListener() {
\r
1976 public void actionPerformed(ActionEvent e) {
\r
1977 modifyPID_actionPerformed(e);
\r
1980 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1981 modifyConservation.addActionListener(new java.awt.event.ActionListener() {
\r
1982 public void actionPerformed(ActionEvent e) {
\r
1983 modifyConservation_actionPerformed(e);
\r
1986 sortByTreeMenu.setLabel("By Tree Order");
\r
1987 sort.setLabel("Sort");
\r
1988 calculate.setLabel("Calculate Tree");
\r
1989 inputText.setLabel("Input from textbox");
\r
1990 inputText.addActionListener(new java.awt.event.ActionListener() {
\r
1991 public void actionPerformed(ActionEvent e) {
\r
1992 inputText_actionPerformed(e);
\r
1996 helpMenu.setLabel("Help");
\r
1997 documentation.setLabel("Documentation");
\r
1998 documentation.addActionListener(new java.awt.event.ActionListener() {
\r
1999 public void actionPerformed(ActionEvent e) {
\r
2000 documentation_actionPerformed(e);
\r
2004 about.setLabel("About...");
\r
2005 about.addActionListener(new java.awt.event.ActionListener() {
\r
2006 public void actionPerformed(ActionEvent e) {
\r
2007 about_actionPerformed(e);
\r
2010 seqLimits.setState(true);
\r
2011 seqLimits.setLabel("Show Sequence Limits");
\r
2012 seqLimits.addItemListener(new ItemListener()
\r
2014 public void itemStateChanged(ItemEvent e)
\r
2016 seqLimits_itemStateChanged(e);
\r
2020 alignFrameMenuBar.add(fileMenu);
\r
2021 alignFrameMenuBar.add(editMenu);
\r
2022 alignFrameMenuBar.add(searchMenu);
\r
2023 alignFrameMenuBar.add(viewMenu);
\r
2024 alignFrameMenuBar.add(colourMenu);
\r
2025 alignFrameMenuBar.add(calculateMenu);
\r
2026 alignFrameMenuBar.add(helpMenu);
\r
2027 fileMenu.add(inputText);
\r
2028 fileMenu.add(outputTextboxMenu);
\r
2029 fileMenu.addSeparator();
\r
2030 fileMenu.add(closeMenuItem);
\r
2031 editMenu.add(undoMenuItem);
\r
2032 editMenu.add(redoMenuItem);
\r
2033 editMenu.add(cut);
\r
2034 editMenu.add(copy);
\r
2035 editMenu.add(Menu1);
\r
2036 editMenu.add(delete);
\r
2037 editMenu.addSeparator();
\r
2038 editMenu.add(selectAllSequenceMenuItem);
\r
2039 editMenu.add(deselectAllSequenceMenuItem);
\r
2040 editMenu.add(invertSequenceMenuItem);
\r
2041 editMenu.add(deleteGroups);
\r
2042 editMenu.addSeparator();
\r
2043 editMenu.add(remove2LeftMenuItem);
\r
2044 editMenu.add(remove2RightMenuItem);
\r
2045 editMenu.add(removeGappedColumnMenuItem);
\r
2046 editMenu.add(removeAllGapsMenuItem);
\r
2047 editMenu.add(removeRedundancyMenuItem);
\r
2048 searchMenu.add(findMenuItem);
\r
2049 viewMenu.add(font);
\r
2050 viewMenu.addSeparator();
\r
2051 viewMenu.add(seqLimits);
\r
2052 viewMenu.addSeparator();
\r
2053 viewMenu.add(wrapMenuItem);
\r
2054 viewMenu.add(scaleAbove);
\r
2055 viewMenu.add(scaleLeft);
\r
2056 viewMenu.add(scaleRight);
\r
2057 viewMenu.addSeparator();
\r
2058 viewMenu.add(viewBoxesMenuItem);
\r
2059 viewMenu.add(viewTextMenuItem);
\r
2060 viewMenu.add(colourTextMenuItem);
\r
2061 viewMenu.add(renderGapsMenuItem);
\r
2062 viewMenu.add(annotationPanelMenuItem);
\r
2063 viewMenu.addSeparator();
\r
2064 viewMenu.add(overviewMenuItem);
\r
2065 colourMenu.add(applyToAllGroups);
\r
2066 colourMenu.addSeparator();
\r
2067 colourMenu.add(noColourmenuItem);
\r
2068 colourMenu.add(clustalColour);
\r
2069 colourMenu.add(BLOSUM62Colour);
\r
2070 colourMenu.add(PIDColour);
\r
2071 colourMenu.add(zappoColour);
\r
2072 colourMenu.add(taylorColour);
\r
2073 colourMenu.add(hydrophobicityColour);
\r
2074 colourMenu.add(helixColour);
\r
2075 colourMenu.add(strandColour);
\r
2076 colourMenu.add(turnColour);
\r
2077 colourMenu.add(buriedColour);
\r
2078 colourMenu.add(nucleotideColour);
\r
2079 colourMenu.add(userDefinedColour);
\r
2080 colourMenu.addSeparator();
\r
2081 colourMenu.add(conservationMenuItem);
\r
2082 colourMenu.add(modifyConservation);
\r
2083 colourMenu.add(abovePIDThreshold);
\r
2084 colourMenu.add(modifyPID);
\r
2085 calculateMenu.add(sort);
\r
2086 calculateMenu.add(calculate);
\r
2087 calculateMenu.addSeparator();
\r
2088 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
2089 calculateMenu.add(PCAMenuItem);
\r
2090 this.add(statusBar, BorderLayout.SOUTH);
\r
2091 Menu1.add(pasteNew);
\r
2092 Menu1.add(pasteThis);
\r
2093 sort.add(sortIDMenuItem);
\r
2094 sort.add(sortByTreeMenu);
\r
2095 sort.add(sortGroupMenuItem);
\r
2096 sort.add(sortPairwiseMenuItem);
\r
2097 calculate.add(averageDistanceTreeMenuItem);
\r
2098 calculate.add(neighbourTreeMenuItem);
\r
2099 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2100 calculate.add(njTreeBlosumMenuItem);
\r
2101 helpMenu.add(documentation);
\r
2102 helpMenu.add(about);
\r