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 implements ActionListener,
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35 ItemListener, KeyListener, MouseListener
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37 public AlignmentPanel alignPanel;
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38 public AlignViewport viewport;
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39 int NEW_WINDOW_WIDTH = 700;
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40 int NEW_WINDOW_HEIGHT = 500;
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41 jalview.bin.JalviewLite applet;
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44 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)
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48 }catch(Exception ex)
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50 ex.printStackTrace();
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53 this.applet = applet;
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54 viewport = new AlignViewport(al, applet);
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55 alignPanel = new AlignmentPanel(this, viewport);
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57 annotationPanelMenuItem.setState(viewport.showAnnotation);
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61 String param = applet.getParameter("sortBy");
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64 if (param.equalsIgnoreCase("Id"))
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65 sortIDMenuItem_actionPerformed();
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66 else if (param.equalsIgnoreCase("Pairwise Identity"))
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67 sortPairwiseMenuItem_actionPerformed();
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70 param = applet.getParameter("wrap");
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73 if (param.equalsIgnoreCase("true"))
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75 wrapMenuItem.setState(true);
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76 wrapMenuItem_actionPerformed();
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82 param = applet.getParameter("windowWidth");
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85 int width = Integer.parseInt(param);
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86 NEW_WINDOW_WIDTH = width;
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88 param = applet.getParameter("windowHeight");
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91 int height = Integer.parseInt(param);
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92 NEW_WINDOW_HEIGHT = height;
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95 catch (Exception ex)
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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(this);
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103 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
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104 alignPanel.idPanel.idCanvas.addKeyListener(this);
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106 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
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108 public void propertyChange(java.beans.PropertyChangeEvent evt)
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110 if (evt.getPropertyName().equals("alignment"))
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112 alignmentChanged();
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118 add(alignPanel, BorderLayout.CENTER);
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119 jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
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121 alignPanel.validate();
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122 alignPanel.repaint();
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124 public AlignViewport getAlignViewport()
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129 public SeqCanvas getSeqcanvas()
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131 return alignPanel.seqPanel.seqCanvas;
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138 * @param String DOCUMENT ME!
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141 public void parseFeaturesFile(String file)
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145 URL url = new URL(file);
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147 BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
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148 SequenceI seq = null;
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149 String line, type, desc, token;
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151 int index, start, end;
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152 StringTokenizer st;
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153 SequenceFeature sf;
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154 FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
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156 while ( (line = in.readLine()) != null)
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159 st = new StringTokenizer(line, "\t");
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160 if (st.countTokens() == 2)
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162 type = st.nextToken();
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163 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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164 fr.setColour(type, ucs.findColour("A"));
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168 while (st.hasMoreElements())
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170 desc = st.nextToken();
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171 token = st.nextToken();
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172 if (!token.equals("ID_NOT_SPECIFIED"))
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174 index = viewport.alignment.findIndex(viewport.alignment.findName(
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180 index = Integer.parseInt(st.nextToken());
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183 start = Integer.parseInt(st.nextToken());
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184 end = Integer.parseInt(st.nextToken());
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186 seq = viewport.alignment.getSequenceAt(index);
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187 start = seq.findIndex(start) - 1;
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188 end = seq.findIndex(end) - 1;
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190 type = st.nextToken();
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192 if(fr.getColour(type)==null)
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194 // Probably the old style groups file
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195 UserColourScheme ucs = new UserColourScheme(type);
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196 fr.setColour(type, ucs.findColour("A"));
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199 sf = new SequenceFeature(type, desc, "", start, end);
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201 seq.addSequenceFeature(sf);
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205 viewport.showSequenceFeatures = true;
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207 alignPanel.repaint();
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210 catch (Exception ex)
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212 System.out.println("Error parsing groups file: " + ex);
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216 public void keyPressed(KeyEvent evt)
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218 switch (evt.getKeyCode())
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220 case 27: // escape key
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221 deselectAllSequenceMenuItem_actionPerformed();
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223 case KeyEvent.VK_X:
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224 if (evt.isControlDown() || evt.isMetaDown())
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226 cut_actionPerformed();
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229 case KeyEvent.VK_C:
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230 if (evt.isControlDown() || evt.isMetaDown())
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232 copy_actionPerformed();
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235 case KeyEvent.VK_V:
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236 if (evt.isControlDown() || evt.isMetaDown())
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241 case KeyEvent.VK_A:
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242 if (evt.isControlDown() || evt.isMetaDown())
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244 selectAllSequenceMenuItem_actionPerformed();
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247 case KeyEvent.VK_DOWN:
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248 moveSelectedSequences(false);
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250 case KeyEvent.VK_UP:
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251 moveSelectedSequences(true);
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253 case KeyEvent.VK_F:
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254 if (evt.isControlDown())
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256 findMenuItem_actionPerformed();
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259 case KeyEvent.VK_BACK_SPACE:
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260 case KeyEvent.VK_DELETE:
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261 cut_actionPerformed();
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265 public void keyReleased(KeyEvent evt)
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267 public void keyTyped(KeyEvent evt)
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270 public void itemStateChanged(ItemEvent evt)
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272 if(evt.getSource()==colourTextMenuItem)
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273 colourTextMenuItem_actionPerformed();
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274 else if(evt.getSource()==wrapMenuItem)
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275 wrapMenuItem_actionPerformed();
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276 else if(evt.getSource()==scaleAbove)
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277 scaleAbove_actionPerformed();
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278 else if(evt.getSource()==scaleLeft)
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279 scaleLeft_actionPerformed();
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280 else if(evt.getSource()==scaleRight)
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281 scaleRight_actionPerformed();
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282 else if(evt.getSource()==seqLimits)
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283 seqLimits_itemStateChanged();
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284 else if(evt.getSource()==viewBoxesMenuItem)
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285 viewBoxesMenuItem_actionPerformed();
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286 else if(evt.getSource()==viewTextMenuItem)
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287 viewTextMenuItem_actionPerformed();
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288 else if(evt.getSource()==renderGapsMenuItem)
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289 renderGapsMenuItem_actionPerformed();
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290 else if(evt.getSource()==annotationPanelMenuItem)
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291 annotationPanelMenuItem_actionPerformed();
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292 else if(evt.getSource()==conservationMenuItem)
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293 conservationMenuItem_actionPerformed();
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294 else if(evt.getSource()==abovePIDThreshold)
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295 abovePIDThreshold_actionPerformed();
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296 else if(evt.getSource()==applyToAllGroups)
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297 applyToAllGroups_actionPerformed();
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299 public void actionPerformed(ActionEvent evt)
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301 if(evt.getSource()==inputText)
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302 inputText_actionPerformed();
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303 else if(evt.getSource()==closeMenuItem)
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304 closeMenuItem_actionPerformed();
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305 else if(evt.getSource()==copy)
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306 copy_actionPerformed();
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307 else if(evt.getSource()==undoMenuItem)
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308 undoMenuItem_actionPerformed();
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309 else if(evt.getSource()==redoMenuItem)
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310 redoMenuItem_actionPerformed();
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311 else if(evt.getSource()==inputText)
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312 inputText_actionPerformed();
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313 else if(evt.getSource()==closeMenuItem)
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314 closeMenuItem_actionPerformed();
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315 else if(evt.getSource()==undoMenuItem)
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316 undoMenuItem_actionPerformed();
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317 else if(evt.getSource()==redoMenuItem)
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318 redoMenuItem_actionPerformed();
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319 else if(evt.getSource()==copy)
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320 copy_actionPerformed();
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321 else if(evt.getSource()==pasteNew)
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322 pasteNew_actionPerformed();
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323 else if(evt.getSource()==pasteThis)
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324 pasteThis_actionPerformed();
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325 else if(evt.getSource()==cut)
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326 cut_actionPerformed();
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327 else if(evt.getSource()==delete)
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328 delete_actionPerformed();
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329 else if(evt.getSource()==deleteGroups)
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330 deleteGroups_actionPerformed();
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331 else if(evt.getSource()==selectAllSequenceMenuItem)
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332 selectAllSequenceMenuItem_actionPerformed();
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333 else if(evt.getSource()==deselectAllSequenceMenuItem)
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334 deselectAllSequenceMenuItem_actionPerformed();
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335 else if(evt.getSource()==invertSequenceMenuItem)
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336 invertSequenceMenuItem_actionPerformed();
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337 else if(evt.getSource()==remove2LeftMenuItem)
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338 remove2LeftMenuItem_actionPerformed();
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339 else if(evt.getSource()==remove2RightMenuItem)
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340 remove2RightMenuItem_actionPerformed();
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341 else if(evt.getSource()==removeGappedColumnMenuItem)
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342 removeGappedColumnMenuItem_actionPerformed();
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343 else if(evt.getSource()==removeAllGapsMenuItem)
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344 removeAllGapsMenuItem_actionPerformed();
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345 else if(evt.getSource()==findMenuItem)
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346 findMenuItem_actionPerformed();
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347 else if(evt.getSource()==font)
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348 font_actionPerformed();
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349 else if(evt.getSource()==overviewMenuItem)
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350 overviewMenuItem_actionPerformed();
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351 else if(evt.getSource()==noColourmenuItem)
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352 noColourmenuItem_actionPerformed();
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353 else if(evt.getSource()==clustalColour)
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354 clustalColour_actionPerformed();
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355 else if(evt.getSource()==zappoColour)
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356 zappoColour_actionPerformed();
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357 else if(evt.getSource()==taylorColour)
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358 taylorColour_actionPerformed();
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359 else if(evt.getSource()==hydrophobicityColour)
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360 hydrophobicityColour_actionPerformed();
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361 else if(evt.getSource()==helixColour)
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362 helixColour_actionPerformed();
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363 else if(evt.getSource()==strandColour)
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364 strandColour_actionPerformed();
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365 else if(evt.getSource()==turnColour)
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366 turnColour_actionPerformed();
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367 else if(evt.getSource()==buriedColour)
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368 buriedColour_actionPerformed();
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369 else if(evt.getSource()==nucleotideColour)
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370 nucleotideColour_actionPerformed();
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371 else if(evt.getSource()==modifyPID)
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372 modifyPID_actionPerformed();
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373 else if(evt.getSource()==modifyConservation)
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374 modifyConservation_actionPerformed();
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375 else if(evt.getSource()==userDefinedColour)
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376 userDefinedColour_actionPerformed();
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377 else if(evt.getSource()==PIDColour)
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378 PIDColour_actionPerformed();
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379 else if(evt.getSource()==BLOSUM62Colour)
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380 BLOSUM62Colour_actionPerformed();
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381 else if(evt.getSource()==sortPairwiseMenuItem)
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382 sortPairwiseMenuItem_actionPerformed();
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383 else if(evt.getSource()==sortIDMenuItem)
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384 sortIDMenuItem_actionPerformed();
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385 else if(evt.getSource()==sortGroupMenuItem)
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386 sortGroupMenuItem_actionPerformed();
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387 else if(evt.getSource()==removeRedundancyMenuItem)
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388 removeRedundancyMenuItem_actionPerformed();
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389 else if(evt.getSource()==pairwiseAlignmentMenuItem)
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390 pairwiseAlignmentMenuItem_actionPerformed();
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391 else if(evt.getSource()==PCAMenuItem)
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392 PCAMenuItem_actionPerformed();
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393 else if(evt.getSource()==averageDistanceTreeMenuItem)
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394 averageDistanceTreeMenuItem_actionPerformed();
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395 else if(evt.getSource()==neighbourTreeMenuItem)
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396 neighbourTreeMenuItem_actionPerformed();
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397 else if(evt.getSource()==njTreeBlosumMenuItem)
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398 njTreeBlosumMenuItem_actionPerformed();
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399 else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
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400 avTreeBlosumMenuItem_actionPerformed();
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401 else if(evt.getSource()==documentation)
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402 documentation_actionPerformed();
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403 else if(evt.getSource()==about)
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404 about_actionPerformed();
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408 public void inputText_actionPerformed()
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410 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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411 Frame frame = new Frame();
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413 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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416 protected void outputText_actionPerformed(ActionEvent e)
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418 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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419 Frame frame = new Frame();
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421 jalview.bin.JalviewLite.addFrame(frame,
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422 "Alignment output - " + e.getActionCommand(),
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424 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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425 viewport.getAlignment().getSequences(),
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426 viewport.showJVSuffix));
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429 public void closeMenuItem_actionPerformed()
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431 PaintRefresher.components.remove(viewport.alignment);
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432 if(PaintRefresher.components.size()==0 && applet==null)
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438 Stack historyList = new Stack();
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439 Stack redoList = new Stack();
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441 void updateEditMenuBar()
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443 if (historyList.size() > 0)
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445 undoMenuItem.setEnabled(true);
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446 HistoryItem hi = (HistoryItem) historyList.peek();
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447 undoMenuItem.setLabel("Undo " + hi.getDescription());
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451 undoMenuItem.setEnabled(false);
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452 undoMenuItem.setLabel("Undo");
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455 if (redoList.size() > 0)
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457 redoMenuItem.setEnabled(true);
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458 HistoryItem hi = (HistoryItem) redoList.peek();
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459 redoMenuItem.setLabel("Redo " + hi.getDescription());
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463 redoMenuItem.setEnabled(false);
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464 redoMenuItem.setLabel("Redo");
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468 public void addHistoryItem(HistoryItem hi)
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470 historyList.push(hi);
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471 updateEditMenuBar();
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474 protected void undoMenuItem_actionPerformed()
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476 HistoryItem hi = (HistoryItem) historyList.pop();
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477 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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478 HistoryItem.HIDE));
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479 restoreHistoryItem(hi);
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480 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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483 protected void redoMenuItem_actionPerformed()
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485 HistoryItem hi = (HistoryItem) redoList.pop();
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486 restoreHistoryItem(hi);
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487 updateEditMenuBar();
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488 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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491 // used by undo and redo
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492 void restoreHistoryItem(HistoryItem hi)
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494 if (hi.getType() == HistoryItem.SORT)
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496 for (int i = 0; i < hi.getSequences().size(); i++)
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498 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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504 for (int i = 0; i < hi.getSequences().size(); i++)
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506 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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507 if (restore.getLength() == 0)
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509 // log.System.out.println(hi.getHidden().elementAt(i));
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510 restore.setSequence(hi.getHidden().elementAt(i).toString());
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511 viewport.alignment.getSequences().insertElementAt(
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513 hi.getAlignIndex(i));
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517 restore.setSequence(hi.getHidden().elementAt(i).toString());
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520 if (hi.getType() == HistoryItem.PASTE)
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522 for (int i = viewport.alignment.getHeight() - 1;
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523 i > hi.getSequences().size() - 1; i--)
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525 viewport.alignment.deleteSequence(i);
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530 updateEditMenuBar();
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532 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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535 public void moveSelectedSequences(boolean up)
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537 SequenceGroup sg = viewport.getSelectionGroup();
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545 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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547 SequenceI seq = viewport.alignment.getSequenceAt(i);
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548 if (!sg.sequences.contains(seq))
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553 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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554 if (sg.sequences.contains(temp))
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559 viewport.alignment.getSequences().setElementAt(temp, i);
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560 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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565 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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567 SequenceI seq = viewport.alignment.getSequenceAt(i);
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568 if (!sg.sequences.contains(seq))
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573 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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574 if (sg.sequences.contains(temp))
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579 viewport.alignment.getSequences().setElementAt(temp, i);
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580 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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584 alignPanel.repaint();
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587 StringBuffer copiedSequences;
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588 protected void copy_actionPerformed()
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590 if (viewport.getSelectionGroup() == null)
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595 SequenceGroup sg = viewport.getSelectionGroup();
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596 copiedSequences = new StringBuffer();
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597 Hashtable orderedSeqs = new Hashtable();
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598 for (int i = 0; i < sg.getSize(); i++)
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600 SequenceI seq = sg.getSequenceAt(i);
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601 int index = viewport.alignment.findIndex(seq);
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602 orderedSeqs.put(index + "", seq);
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605 int index = 0, startRes, endRes;
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608 for (int i = 0; i < sg.getSize(); i++)
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610 SequenceI seq = null;
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612 while (seq == null)
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614 if (orderedSeqs.containsKey(index + ""))
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616 seq = (SequenceI) orderedSeqs.get(index + "");
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628 //Returns residue following index if gap
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629 startRes = seq.findPosition(sg.getStartRes());
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632 //Need to find the residue preceeding index if gap
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635 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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637 ch = seq.getCharAt(j);
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638 if (!jalview.util.Comparison.isGap( (ch)))
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646 endRes += seq.getStart() -1;
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649 copiedSequences.append(seq.getName() + "\t" +
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652 seq.getSequence(sg.getStartRes(),
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653 sg.getEndRes() + 1) + "\n");
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658 protected void pasteNew_actionPerformed()
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663 protected void pasteThis_actionPerformed()
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665 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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666 HistoryItem.PASTE));
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670 void paste(boolean newAlignment)
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674 if (copiedSequences == null)
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679 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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680 Vector seqs = new Vector();
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681 while (st.hasMoreElements())
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683 String name = st.nextToken();
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684 int start = Integer.parseInt(st.nextToken());
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685 int end = Integer.parseInt(st.nextToken());
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686 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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690 viewport.alignment.addSequence(sequence);
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694 seqs.addElement(sequence);
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700 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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701 for (int i = 0; i < seqs.size(); i++)
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703 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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706 String newtitle = new String("Copied sequences");
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707 if (getTitle().startsWith("Copied sequences"))
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709 newtitle = getTitle();
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713 newtitle = newtitle.concat("- from " + getTitle());
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715 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
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717 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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718 NEW_WINDOW_HEIGHT);
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722 viewport.setEndSeq(viewport.alignment.getHeight());
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723 viewport.alignment.getWidth();
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724 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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728 catch (Exception ex)
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729 {} // could be anything being pasted in here
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733 protected void cut_actionPerformed()
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735 copy_actionPerformed();
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736 delete_actionPerformed();
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739 protected void delete_actionPerformed()
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741 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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742 HistoryItem.HIDE));
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743 if (viewport.getSelectionGroup() == null)
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749 SequenceGroup sg = viewport.getSelectionGroup();
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750 boolean allSequences = false;
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751 if(sg.sequences.size()==viewport.alignment.getHeight())
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752 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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768 if (seq.getSequence().length() < 1)
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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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780 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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781 if (viewport.getAlignment().getHeight() < 1)
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785 this.setVisible(false);
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787 catch (Exception ex)
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790 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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794 protected void deleteGroups_actionPerformed()
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796 viewport.alignment.deleteAllGroups();
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797 viewport.setSelectionGroup(null);
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799 alignPanel.repaint();
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802 public void selectAllSequenceMenuItem_actionPerformed()
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804 SequenceGroup sg = new SequenceGroup();
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805 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
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807 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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809 sg.setEndRes(viewport.alignment.getWidth()-1);
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810 viewport.setSelectionGroup(sg);
\r
811 alignPanel.repaint();
\r
812 PaintRefresher.Refresh(null, viewport.alignment);
\r
815 public void deselectAllSequenceMenuItem_actionPerformed()
\r
817 viewport.setSelectionGroup(null);
\r
818 viewport.getColumnSelection().clear();
\r
819 viewport.setSelectionGroup(null);
\r
820 alignPanel.idPanel.idCanvas.searchResults = null;
\r
821 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
822 alignPanel.repaint();
\r
823 PaintRefresher.Refresh(null, viewport.alignment);
\r
826 public void invertSequenceMenuItem_actionPerformed()
\r
828 SequenceGroup sg = viewport.getSelectionGroup();
\r
829 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
831 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
834 PaintRefresher.Refresh(null, viewport.alignment);
\r
837 public void remove2LeftMenuItem_actionPerformed()
\r
839 ColumnSelection colSel = viewport.getColumnSelection();
\r
840 if (colSel.size() > 0)
\r
842 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
843 HistoryItem.HIDE));
\r
844 int min = colSel.getMin();
\r
845 viewport.getAlignment().trimLeft(min);
\r
846 colSel.compensateForEdit(0, min);
\r
848 if (viewport.getSelectionGroup() != null)
\r
850 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
853 Vector groups = viewport.alignment.getGroups();
\r
854 for (int i = 0; i < groups.size(); i++)
\r
856 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
857 if (!sg.adjustForRemoveLeft(min))
\r
859 viewport.alignment.deleteGroup(sg);
\r
862 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
866 public void remove2RightMenuItem_actionPerformed()
\r
868 ColumnSelection colSel = viewport.getColumnSelection();
\r
869 if (colSel.size() > 0)
\r
871 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
872 HistoryItem.HIDE));
\r
873 int max = colSel.getMax();
\r
874 viewport.getAlignment().trimRight(max);
\r
875 if (viewport.getSelectionGroup() != null)
\r
877 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
880 Vector groups = viewport.alignment.getGroups();
\r
881 for (int i = 0; i < groups.size(); i++)
\r
883 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
884 if (!sg.adjustForRemoveRight(max))
\r
886 viewport.alignment.deleteGroup(sg);
\r
889 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
894 public void removeGappedColumnMenuItem_actionPerformed()
\r
896 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
897 viewport.alignment,
\r
898 HistoryItem.HIDE));
\r
900 //This is to maintain viewport position on first residue
\r
901 //of first sequence
\r
902 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
903 int startRes = seq.findPosition(viewport.startRes);
\r
905 viewport.getAlignment().removeGaps();
\r
907 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
909 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
912 public void removeAllGapsMenuItem_actionPerformed()
\r
914 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
915 HistoryItem.HIDE));
\r
917 //This is to maintain viewport position on first residue
\r
918 //of first sequence
\r
919 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
920 int startRes = seq.findPosition(viewport.startRes);
\r
927 int start=0, end = viewport.alignment.getWidth();
\r
929 if (viewport.getSelectionGroup() != null
\r
930 && viewport.getSelectionGroup().sequences != null
\r
931 && viewport.getSelectionGroup().sequences.size()>0)
\r
933 seqs = viewport.getSelectionGroup().sequences;
\r
934 start = viewport.getSelectionGroup().getStartRes();
\r
935 end = viewport.getSelectionGroup().getEndRes()+1;
\r
938 seqs = viewport.alignment.getSequences();
\r
940 for (int i = 0; i < seqs.size(); i++)
\r
942 current = (SequenceI) seqs.elementAt(i);
\r
943 jSize = current.getLength();
\r
945 // Removing a range is much quicker than removing gaps
\r
946 // one by one for long sequences
\r
948 int rangeStart=-1, rangeEnd=-1;
\r
952 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
969 current.deleteChars(rangeStart, rangeEnd);
\r
970 j-=rangeEnd-rangeStart;
\r
971 jSize-=rangeEnd-rangeStart;
\r
979 while (j < end && j < jSize);
\r
982 current.deleteChars(rangeStart, rangeEnd);
\r
985 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
986 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
989 public void alignmentChanged()
\r
991 viewport.updateConsensus();
\r
992 viewport.updateConservation ();
\r
993 resetAllColourSchemes();
\r
994 if(alignPanel.overviewPanel!=null)
\r
995 alignPanel.overviewPanel.updateOverviewImage();
\r
997 viewport.alignment.adjustSequenceAnnotations();
\r
998 alignPanel.repaint();
\r
1001 void resetAllColourSchemes()
\r
1003 ColourSchemeI cs = viewport.globalColourScheme;
\r
1006 if (cs instanceof ClustalxColourScheme)
\r
1008 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1009 resetClustalX(viewport.alignment.getSequences(),
\r
1010 viewport.alignment.getWidth());
\r
1013 cs.setConsensus(viewport.vconsensus);
\r
1014 if (cs.conservationApplied())
\r
1016 Alignment al = (Alignment) viewport.alignment;
\r
1017 Conservation c = new Conservation("All",
\r
1018 ResidueProperties.propHash, 3,
\r
1019 al.getSequences(), 0,
\r
1020 al.getWidth() - 1);
\r
1022 c.verdict(false, viewport.ConsPercGaps);
\r
1024 cs.setConservation(c);
\r
1028 int s, sSize = viewport.alignment.getGroups().size();
\r
1029 for(s=0; s<sSize; s++)
\r
1031 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1032 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1034 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1036 sg.recalcConservation();
\r
1042 public void findMenuItem_actionPerformed()
\r
1044 new Finder(alignPanel);
\r
1047 public void font_actionPerformed()
\r
1049 new FontChooser(alignPanel);
\r
1053 public void seqLimits_itemStateChanged()
\r
1055 viewport.setShowJVSuffix(seqLimits.getState());
\r
1056 alignPanel.fontChanged();
\r
1057 alignPanel.repaint();
\r
1061 protected void colourTextMenuItem_actionPerformed()
\r
1063 viewport.setColourText(colourTextMenuItem.getState());
\r
1064 alignPanel.repaint();
\r
1067 protected void wrapMenuItem_actionPerformed()
\r
1069 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1070 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1071 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1072 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1073 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1074 alignPanel.repaint();
\r
1077 protected void scaleAbove_actionPerformed()
\r
1079 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1080 alignPanel.repaint();
\r
1083 protected void scaleLeft_actionPerformed()
\r
1085 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1086 alignPanel.repaint();
\r
1089 protected void scaleRight_actionPerformed()
\r
1091 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1092 alignPanel.repaint();
\r
1095 public void viewBoxesMenuItem_actionPerformed()
\r
1097 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1098 alignPanel.repaint();
\r
1101 public void viewTextMenuItem_actionPerformed()
\r
1103 viewport.setShowText(viewTextMenuItem.getState());
\r
1104 alignPanel.repaint();
\r
1107 protected void renderGapsMenuItem_actionPerformed()
\r
1109 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1110 alignPanel.repaint();
\r
1113 public void annotationPanelMenuItem_actionPerformed()
\r
1115 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1116 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1119 public void overviewMenuItem_actionPerformed()
\r
1121 if (alignPanel.overviewPanel != null)
\r
1126 Frame frame = new Frame();
\r
1127 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1128 frame.add(overview);
\r
1129 // +50 must allow for applet frame window
\r
1130 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1131 overview.preferredSize().width,
\r
1132 overview.preferredSize().height + 50);
\r
1135 frame.addWindowListener(new WindowAdapter()
\r
1137 public void windowClosing(WindowEvent e)
\r
1139 alignPanel.setOverviewPanel(null);
\r
1143 alignPanel.setOverviewPanel(overview);
\r
1147 protected void noColourmenuItem_actionPerformed()
\r
1149 changeColour(null);
\r
1152 public void clustalColour_actionPerformed()
\r
1154 abovePIDThreshold.setState(false);
\r
1155 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1156 viewport.alignment.getWidth()));
\r
1159 public void zappoColour_actionPerformed()
\r
1161 changeColour(new ZappoColourScheme());
\r
1164 public void taylorColour_actionPerformed()
\r
1166 changeColour(new TaylorColourScheme());
\r
1169 public void hydrophobicityColour_actionPerformed()
\r
1171 changeColour(new HydrophobicColourScheme());
\r
1174 public void helixColour_actionPerformed()
\r
1176 changeColour(new HelixColourScheme());
\r
1179 public void strandColour_actionPerformed()
\r
1181 changeColour(new StrandColourScheme());
\r
1184 public void turnColour_actionPerformed()
\r
1186 changeColour(new TurnColourScheme());
\r
1189 public void buriedColour_actionPerformed()
\r
1191 changeColour(new BuriedColourScheme());
\r
1194 public void nucleotideColour_actionPerformed()
\r
1196 changeColour(new NucleotideColourScheme());
\r
1199 protected void applyToAllGroups_actionPerformed()
\r
1201 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1204 void changeColour(ColourSchemeI cs)
\r
1206 int threshold = 0;
\r
1210 if (viewport.getAbovePIDThreshold())
\r
1212 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1214 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1216 viewport.setGlobalColourScheme(cs);
\r
1220 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1223 if (viewport.getConservationSelected())
\r
1226 Alignment al = (Alignment) viewport.alignment;
\r
1227 Conservation c = new Conservation("All",
\r
1228 ResidueProperties.propHash, 3,
\r
1229 al.getSequences(), 0,
\r
1230 al.getWidth() - 1);
\r
1233 c.verdict(false, viewport.ConsPercGaps);
\r
1235 cs.setConservation(c);
\r
1237 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1243 cs.setConservation(null);
\r
1246 cs.setConsensus(viewport.vconsensus);
\r
1249 viewport.setGlobalColourScheme(cs);
\r
1251 if (viewport.getColourAppliesToAllGroups())
\r
1253 Vector groups = viewport.alignment.getGroups();
\r
1254 for (int i = 0; i < groups.size(); i++)
\r
1256 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1263 if (cs instanceof ClustalxColourScheme)
\r
1265 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1271 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1273 catch (Exception ex)
\r
1275 ex.printStackTrace();
\r
1280 if (viewport.getAbovePIDThreshold()
\r
1281 || cs instanceof PIDColourScheme
\r
1282 || cs instanceof Blosum62ColourScheme)
\r
1284 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1285 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1288 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1290 if (viewport.getConservationSelected())
\r
1292 Conservation c = new Conservation("Group",
\r
1293 ResidueProperties.propHash, 3,
\r
1295 viewport.alignment.getWidth() - 1);
\r
1297 c.verdict(false, viewport.ConsPercGaps);
\r
1298 sg.cs.setConservation(c);
\r
1302 sg.cs.setConservation(null);
\r
1303 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1310 if (alignPanel.getOverviewPanel() != null)
\r
1312 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1315 alignPanel.repaint();
\r
1320 protected void modifyPID_actionPerformed()
\r
1322 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1324 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1326 SliderPanel.showPIDSlider();
\r
1330 protected void modifyConservation_actionPerformed()
\r
1332 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1334 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1336 SliderPanel.showConservationSlider();
\r
1340 protected void conservationMenuItem_actionPerformed()
\r
1342 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1344 viewport.setAbovePIDThreshold(false);
\r
1345 abovePIDThreshold.setState(false);
\r
1347 changeColour(viewport.getGlobalColourScheme());
\r
1349 modifyConservation_actionPerformed();
\r
1352 public void abovePIDThreshold_actionPerformed()
\r
1354 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1356 conservationMenuItem.setState(false);
\r
1357 viewport.setConservationSelected(false);
\r
1359 changeColour(viewport.getGlobalColourScheme());
\r
1361 modifyPID_actionPerformed();
\r
1364 public void userDefinedColour_actionPerformed()
\r
1366 new UserDefinedColours(alignPanel, null);
\r
1369 public void PIDColour_actionPerformed()
\r
1371 changeColour(new PIDColourScheme());
\r
1374 public void BLOSUM62Colour_actionPerformed()
\r
1376 changeColour(new Blosum62ColourScheme());
\r
1379 public void sortPairwiseMenuItem_actionPerformed()
\r
1381 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1382 HistoryItem.SORT));
\r
1383 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1384 viewport.getAlignment().getSequenceAt(0));
\r
1385 alignPanel.repaint();
\r
1388 public void sortIDMenuItem_actionPerformed()
\r
1390 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1391 HistoryItem.SORT));
\r
1392 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1393 alignPanel.repaint();
\r
1396 public void sortGroupMenuItem_actionPerformed()
\r
1398 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1399 HistoryItem.SORT));
\r
1400 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1401 alignPanel.repaint();
\r
1405 public void removeRedundancyMenuItem_actionPerformed()
\r
1407 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1408 Frame frame = new Frame();
\r
1410 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1415 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1417 if (viewport.getSelectionGroup().getSize() > 1)
\r
1419 Frame frame = new Frame();
\r
1420 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1421 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1425 public void PCAMenuItem_actionPerformed()
\r
1427 //are the sequences aligned?
\r
1428 if (!viewport.alignment.isAligned())
\r
1430 SequenceI current;
\r
1431 int Width = viewport.getAlignment().getWidth();
\r
1433 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1436 current = viewport.getAlignment().getSequenceAt(i);
\r
1438 if (current.getLength() < Width)
\r
1440 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1443 alignPanel.repaint();
\r
1446 if ( (viewport.getSelectionGroup() != null &&
\r
1447 viewport.getSelectionGroup().getSize() < 4 &&
\r
1448 viewport.getSelectionGroup().getSize() > 0)
\r
1449 || viewport.getAlignment().getHeight() < 4)
\r
1456 new PCAPanel(viewport);
\r
1458 catch (java.lang.OutOfMemoryError ex)
\r
1464 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1466 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1469 public void neighbourTreeMenuItem_actionPerformed()
\r
1471 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1474 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1476 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1479 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1481 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1484 void NewTreePanel(String type, String pwType, String title)
\r
1486 //are the sequences aligned?
\r
1487 if (!viewport.alignment.isAligned())
\r
1489 SequenceI current;
\r
1490 int Width = viewport.getAlignment().getWidth();
\r
1492 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1495 current = viewport.getAlignment().getSequenceAt(i);
\r
1497 if (current.getLength() < Width)
\r
1499 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1502 alignPanel.repaint();
\r
1506 final TreePanel tp;
\r
1507 if (viewport.getSelectionGroup() != null &&
\r
1508 viewport.getSelectionGroup().getSize() > 3)
\r
1510 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1512 0, viewport.alignment.getWidth());
\r
1516 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1517 type, pwType, 0, viewport.alignment.getWidth());
\r
1520 addTreeMenuItem(tp, title);
\r
1522 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1525 public void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1527 final MenuItem item = new MenuItem(title);
\r
1528 sortByTreeMenu.add(item);
\r
1529 item.addActionListener(new java.awt.event.ActionListener()
\r
1531 public void actionPerformed(ActionEvent evt)
\r
1533 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1534 HistoryItem.SORT));
\r
1535 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1536 alignPanel.repaint();
\r
1540 treePanel.addWindowListener(new WindowAdapter()
\r
1542 public void windowClosing(WindowEvent e)
\r
1544 sortByTreeMenu.remove(item);
\r
1549 protected void documentation_actionPerformed()
\r
1551 showURL("http://www.jalview.org/help.html", "HELP");
\r
1554 protected void about_actionPerformed()
\r
1557 class AboutPanel extends Canvas
\r
1560 public AboutPanel(String version)
\r
1561 { this.version = version; }
\r
1563 public void paint(Graphics g)
\r
1565 g.setColor(Color.white);
\r
1566 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1567 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1568 FontMetrics fm = g.getFontMetrics();
\r
1569 int fh = fm.getHeight();
\r
1571 g.setColor(Color.black);
\r
1572 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1573 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1574 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1575 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1577 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1580 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1582 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1583 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1585 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1589 String version = "test";
\r
1590 java.net.URL url = getClass().getResource("/.build_properties");
\r
1595 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1596 url.openStream()));
\r
1598 while ( (line = reader.readLine()) != null)
\r
1600 if (line.indexOf("VERSION") > -1)
\r
1602 version = line.substring(line.indexOf("=") + 1);
\r
1606 catch (Exception ex)
\r
1608 ex.printStackTrace();
\r
1613 Frame frame = new Frame();
\r
1614 frame.add(new AboutPanel(version));
\r
1615 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1619 public void showURL(String url, String target)
\r
1621 if (applet == null)
\r
1623 System.out.println("Not running as applet - no browser available.");
\r
1629 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1632 catch (Exception ex)
\r
1634 ex.printStackTrace();
\r
1640 //////////////////////////////////////////////////////////////////////////////////
\r
1641 //JBuilder Graphics here
\r
1643 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1644 protected Menu fileMenu = new Menu();
\r
1645 protected MenuItem closeMenuItem = new MenuItem();
\r
1646 protected Menu editMenu = new Menu();
\r
1647 protected Menu viewMenu = new Menu();
\r
1648 protected Menu colourMenu = new Menu();
\r
1649 protected Menu calculateMenu = new Menu();
\r
1650 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
\r
1651 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
\r
1652 protected MenuItem invertSequenceMenuItem = new MenuItem();
\r
1653 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1654 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1655 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1656 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1657 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1658 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1659 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1660 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1661 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1662 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1663 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1664 protected MenuItem PCAMenuItem = new MenuItem();
\r
1665 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1666 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1667 BorderLayout borderLayout1 = new BorderLayout();
\r
1668 public Label statusBar = new Label();
\r
1669 protected Menu outputTextboxMenu = new Menu();
\r
1670 protected MenuItem clustalColour = new MenuItem();
\r
1671 protected MenuItem zappoColour = new MenuItem();
\r
1672 protected MenuItem taylorColour = new MenuItem();
\r
1673 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1674 protected MenuItem helixColour = new MenuItem();
\r
1675 protected MenuItem strandColour = new MenuItem();
\r
1676 protected MenuItem turnColour = new MenuItem();
\r
1677 protected MenuItem buriedColour = new MenuItem();
\r
1678 protected MenuItem userDefinedColour = new MenuItem();
\r
1679 protected MenuItem PIDColour = new MenuItem();
\r
1680 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1681 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1682 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1683 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1684 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1685 MenuItem overviewMenuItem = new MenuItem();
\r
1686 protected MenuItem undoMenuItem = new MenuItem();
\r
1687 protected MenuItem redoMenuItem = new MenuItem();
\r
1688 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1689 MenuItem noColourmenuItem = new MenuItem();
\r
1690 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1691 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1692 MenuItem findMenuItem = new MenuItem();
\r
1693 Menu searchMenu = new Menu();
\r
1694 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1695 protected MenuItem nucleotideColour = new MenuItem();
\r
1696 MenuItem deleteGroups = new MenuItem();
\r
1697 MenuItem delete = new MenuItem();
\r
1698 MenuItem copy = new MenuItem();
\r
1699 MenuItem cut = new MenuItem();
\r
1700 Menu pasteMenu = new Menu();
\r
1701 MenuItem pasteNew = new MenuItem();
\r
1702 MenuItem pasteThis = new MenuItem();
\r
1703 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1704 protected MenuItem font = new MenuItem();
\r
1705 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1706 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1707 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1708 MenuItem modifyPID = new MenuItem();
\r
1709 MenuItem modifyConservation = new MenuItem();
\r
1710 protected Menu sortByTreeMenu = new Menu();
\r
1711 Menu sort = new Menu();
\r
1712 Menu calculate = new Menu();
\r
1713 MenuItem inputText = new MenuItem();
\r
1714 Menu helpMenu = new Menu();
\r
1715 MenuItem documentation = new MenuItem();
\r
1716 MenuItem about = new MenuItem();
\r
1717 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1718 Panel embeddedMenu;
\r
1719 Label embeddedEdit;
\r
1720 Label embeddedSearch;
\r
1721 Label embeddedView;
\r
1722 Label embeddedColour;
\r
1723 Label embeddedFile;
\r
1724 Label embeddedHelp;
\r
1725 Label embeddedCalculate;
\r
1726 FlowLayout flowLayout1;
\r
1728 private void jbInit() throws Exception {
\r
1730 setMenuBar(alignFrameMenuBar);
\r
1734 // dynamically fill save as menu with available formats
\r
1735 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1738 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1741 item.addActionListener(new java.awt.event.ActionListener()
\r
1743 public void actionPerformed(ActionEvent e)
\r
1745 outputText_actionPerformed(e);
\r
1749 outputTextboxMenu.add(item);
\r
1752 fileMenu.setLabel("File");
\r
1753 closeMenuItem.setLabel("Close");
\r
1754 closeMenuItem.addActionListener(this);
\r
1755 editMenu.setLabel("Edit");
\r
1756 viewMenu.setLabel("View");
\r
1757 colourMenu.setLabel("Colour");
\r
1758 calculateMenu.setLabel("Calculate");
\r
1759 selectAllSequenceMenuItem.setLabel("Select all");
\r
1760 selectAllSequenceMenuItem.addActionListener(this);
\r
1761 deselectAllSequenceMenuItem.setLabel("Deselect All");
\r
1762 deselectAllSequenceMenuItem.addActionListener(this);
\r
1763 invertSequenceMenuItem.setLabel("Invert Selection");
\r
1764 invertSequenceMenuItem.addActionListener(this);
\r
1765 remove2LeftMenuItem.setLabel("Remove Left");
\r
1766 remove2LeftMenuItem.addActionListener(this);
\r
1767 remove2RightMenuItem.setLabel("Remove Right");
\r
1768 remove2RightMenuItem.addActionListener(this);
\r
1769 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1770 removeGappedColumnMenuItem.addActionListener(this);
\r
1771 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1772 removeAllGapsMenuItem.addActionListener(this);
\r
1773 viewBoxesMenuItem.setLabel("Boxes");
\r
1774 viewBoxesMenuItem.setState(true);
\r
1775 viewBoxesMenuItem.addItemListener(this);
\r
1776 viewTextMenuItem.setLabel("Text");
\r
1777 viewTextMenuItem.setState(true);
\r
1778 viewTextMenuItem.addItemListener(this);
\r
1779 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1780 sortPairwiseMenuItem.addActionListener(this);
\r
1781 sortIDMenuItem.setLabel("by ID");
\r
1782 sortIDMenuItem.addActionListener(this);
\r
1783 sortGroupMenuItem.setLabel("by Group");
\r
1784 sortGroupMenuItem.addActionListener(this);
\r
1785 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1786 removeRedundancyMenuItem.addActionListener(this);
\r
1787 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1788 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1789 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1790 PCAMenuItem.addActionListener(this);
\r
1791 averageDistanceTreeMenuItem.setLabel(
\r
1792 "Average Distance Using % Identity");
\r
1793 averageDistanceTreeMenuItem.addActionListener(this);
\r
1794 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1795 neighbourTreeMenuItem.addActionListener(this);
\r
1796 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1797 statusBar.setBackground(Color.white);
\r
1798 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1799 statusBar.setText("Status bar");
\r
1800 outputTextboxMenu.setLabel("Output to Textbox");
\r
1801 clustalColour.setLabel("Clustalx");
\r
1803 clustalColour.addActionListener(this);
\r
1804 zappoColour.setLabel("Zappo");
\r
1805 zappoColour.addActionListener(this);
\r
1806 taylorColour.setLabel("Taylor");
\r
1807 taylorColour.addActionListener(this);
\r
1808 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1809 hydrophobicityColour.addActionListener(this);
\r
1810 helixColour.setLabel("Helix Propensity");
\r
1811 helixColour.addActionListener(this);
\r
1812 strandColour.setLabel("Strand Propensity");
\r
1813 strandColour.addActionListener(this);
\r
1814 turnColour.setLabel("Turn Propensity");
\r
1815 turnColour.addActionListener(this);
\r
1816 buriedColour.setLabel("Buried Index");
\r
1817 buriedColour.addActionListener(this);
\r
1818 userDefinedColour.setLabel("User Defined...");
\r
1819 userDefinedColour.addActionListener(this);
\r
1820 PIDColour.setLabel("Percentage Identity");
\r
1821 PIDColour.addActionListener(this);
\r
1822 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1823 BLOSUM62Colour.addActionListener(this);
\r
1824 avDistanceTreeBlosumMenuItem.setLabel(
\r
1825 "Average Distance Using BLOSUM62");
\r
1826 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1827 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1828 njTreeBlosumMenuItem.addActionListener(this);
\r
1829 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1830 annotationPanelMenuItem.addItemListener(this);
\r
1831 colourTextMenuItem.setLabel("Colour Text");
\r
1832 colourTextMenuItem.addItemListener(this);
\r
1833 overviewMenuItem.setLabel("Overview Window");
\r
1834 overviewMenuItem.addActionListener(this);
\r
1835 undoMenuItem.setEnabled(false);
\r
1836 undoMenuItem.setLabel("Undo");
\r
1837 undoMenuItem.addActionListener(this);
\r
1838 redoMenuItem.setEnabled(false);
\r
1839 redoMenuItem.setLabel("Redo");
\r
1840 redoMenuItem.addActionListener(this);
\r
1841 conservationMenuItem.setLabel("by Conservation");
\r
1842 conservationMenuItem.addItemListener(this);
\r
1843 noColourmenuItem.setLabel("None");
\r
1844 noColourmenuItem.addActionListener(this);
\r
1845 wrapMenuItem.setLabel("Wrap");
\r
1846 wrapMenuItem.addItemListener(this);
\r
1847 renderGapsMenuItem.setLabel("Show Gaps");
\r
1848 renderGapsMenuItem.setState(true);
\r
1849 renderGapsMenuItem.addItemListener(this);
\r
1850 findMenuItem.setLabel("Find...");
\r
1851 findMenuItem.addActionListener(this);
\r
1852 searchMenu.setLabel("Search");
\r
1854 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1855 abovePIDThreshold.addItemListener(this);
\r
1856 nucleotideColour.setLabel("Nucleotide");
\r
1857 nucleotideColour.addActionListener(this);
\r
1858 deleteGroups.setLabel("Undefine Groups");
\r
1859 deleteGroups.addActionListener(this);
\r
1860 copy.setLabel("Copy");
\r
1861 copy.addActionListener(this);
\r
1862 cut.setLabel("Cut");
\r
1863 cut.addActionListener(this);
\r
1864 delete.setLabel("Delete");
\r
1865 delete.addActionListener(this);
\r
1866 pasteMenu.setLabel("Paste");
\r
1867 pasteNew.setLabel("To New Alignment");
\r
1868 pasteNew.addActionListener(this);
\r
1869 pasteThis.setLabel("Add To This Alignment");
\r
1870 pasteThis.addActionListener(this);
\r
1871 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1872 applyToAllGroups.setState(true);
\r
1873 applyToAllGroups.addItemListener(this);
\r
1874 font.setLabel("Font...");
\r
1875 font.addActionListener(this);
\r
1876 scaleAbove.setLabel("Scale Above");
\r
1877 scaleAbove.setState(true);
\r
1878 scaleAbove.setEnabled(false);
\r
1879 scaleAbove.addItemListener(this);
\r
1880 scaleLeft.setEnabled(false);
\r
1881 scaleLeft.setState(true);
\r
1882 scaleLeft.setLabel("Scale Left");
\r
1883 scaleLeft.addItemListener(this);
\r
1884 scaleRight.setEnabled(false);
\r
1885 scaleRight.setState(true);
\r
1886 scaleRight.setLabel("Scale Right");
\r
1887 scaleRight.addItemListener(this);
\r
1888 modifyPID.setLabel("Modify Identity Threshold...");
\r
1889 modifyPID.addActionListener(this);
\r
1890 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1891 modifyConservation.addActionListener(this);
\r
1892 sortByTreeMenu.setLabel("By Tree Order");
\r
1893 sort.setLabel("Sort");
\r
1894 calculate.setLabel("Calculate Tree");
\r
1895 inputText.setLabel("Input from textbox");
\r
1896 inputText.addActionListener(this);
\r
1898 helpMenu.setLabel("Help");
\r
1899 documentation.setLabel("Documentation");
\r
1900 documentation.addActionListener(this);
\r
1902 about.setLabel("About...");
\r
1903 about.addActionListener(this);
\r
1904 seqLimits.setState(true);
\r
1905 seqLimits.setLabel("Show Sequence Limits");
\r
1906 seqLimits.addItemListener(this);
\r
1908 alignFrameMenuBar.add(fileMenu);
\r
1909 alignFrameMenuBar.add(editMenu);
\r
1910 alignFrameMenuBar.add(searchMenu);
\r
1911 alignFrameMenuBar.add(viewMenu);
\r
1912 alignFrameMenuBar.add(colourMenu);
\r
1913 alignFrameMenuBar.add(calculateMenu);
\r
1914 alignFrameMenuBar.add(helpMenu);
\r
1915 fileMenu.add(inputText);
\r
1916 fileMenu.add(outputTextboxMenu);
\r
1917 fileMenu.addSeparator();
\r
1918 fileMenu.add(closeMenuItem);
\r
1919 editMenu.add(undoMenuItem);
\r
1920 editMenu.add(redoMenuItem);
\r
1921 editMenu.add(cut);
\r
1922 editMenu.add(copy);
\r
1923 editMenu.add(pasteMenu);
\r
1924 editMenu.add(delete);
\r
1925 editMenu.addSeparator();
\r
1926 editMenu.add(selectAllSequenceMenuItem);
\r
1927 editMenu.add(deselectAllSequenceMenuItem);
\r
1928 editMenu.add(invertSequenceMenuItem);
\r
1929 editMenu.add(deleteGroups);
\r
1930 editMenu.addSeparator();
\r
1931 editMenu.add(remove2LeftMenuItem);
\r
1932 editMenu.add(remove2RightMenuItem);
\r
1933 editMenu.add(removeGappedColumnMenuItem);
\r
1934 editMenu.add(removeAllGapsMenuItem);
\r
1935 editMenu.add(removeRedundancyMenuItem);
\r
1936 searchMenu.add(findMenuItem);
\r
1937 viewMenu.add(font);
\r
1938 viewMenu.addSeparator();
\r
1939 viewMenu.add(seqLimits);
\r
1940 viewMenu.addSeparator();
\r
1941 viewMenu.add(wrapMenuItem);
\r
1942 viewMenu.add(scaleAbove);
\r
1943 viewMenu.add(scaleLeft);
\r
1944 viewMenu.add(scaleRight);
\r
1945 viewMenu.addSeparator();
\r
1946 viewMenu.add(viewBoxesMenuItem);
\r
1947 viewMenu.add(viewTextMenuItem);
\r
1948 viewMenu.add(colourTextMenuItem);
\r
1949 viewMenu.add(renderGapsMenuItem);
\r
1950 viewMenu.add(annotationPanelMenuItem);
\r
1951 viewMenu.addSeparator();
\r
1952 viewMenu.add(overviewMenuItem);
\r
1953 colourMenu.add(applyToAllGroups);
\r
1954 colourMenu.addSeparator();
\r
1955 colourMenu.add(noColourmenuItem);
\r
1956 colourMenu.add(clustalColour);
\r
1957 colourMenu.add(BLOSUM62Colour);
\r
1958 colourMenu.add(PIDColour);
\r
1959 colourMenu.add(zappoColour);
\r
1960 colourMenu.add(taylorColour);
\r
1961 colourMenu.add(hydrophobicityColour);
\r
1962 colourMenu.add(helixColour);
\r
1963 colourMenu.add(strandColour);
\r
1964 colourMenu.add(turnColour);
\r
1965 colourMenu.add(buriedColour);
\r
1966 colourMenu.add(nucleotideColour);
\r
1967 colourMenu.add(userDefinedColour);
\r
1968 colourMenu.addSeparator();
\r
1969 colourMenu.add(conservationMenuItem);
\r
1970 colourMenu.add(modifyConservation);
\r
1971 colourMenu.add(abovePIDThreshold);
\r
1972 colourMenu.add(modifyPID);
\r
1973 calculateMenu.add(sort);
\r
1974 calculateMenu.add(calculate);
\r
1975 calculateMenu.addSeparator();
\r
1976 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1977 calculateMenu.add(PCAMenuItem);
\r
1978 this.add(statusBar, BorderLayout.SOUTH);
\r
1979 pasteMenu.add(pasteNew);
\r
1980 pasteMenu.add(pasteThis);
\r
1981 sort.add(sortIDMenuItem);
\r
1982 sort.add(sortByTreeMenu);
\r
1983 sort.add(sortGroupMenuItem);
\r
1984 sort.add(sortPairwiseMenuItem);
\r
1985 calculate.add(averageDistanceTreeMenuItem);
\r
1986 calculate.add(neighbourTreeMenuItem);
\r
1987 calculate.add(avDistanceTreeBlosumMenuItem);
\r
1988 calculate.add(njTreeBlosumMenuItem);
\r
1989 helpMenu.add(documentation);
\r
1990 helpMenu.add(about);
\r
1993 public void setEmbedded()
\r
1996 embeddedMenu = new Panel();
\r
1997 embeddedEdit = new Label();
\r
1998 embeddedSearch = new Label();
\r
1999 embeddedView = new Label();
\r
2000 embeddedColour = new Label();
\r
2001 embeddedFile = new Label();
\r
2002 embeddedHelp = new Label();
\r
2003 embeddedCalculate = new Label();
\r
2004 flowLayout1 = new FlowLayout();
\r
2005 embeddedMenu.setBackground(Color.lightGray);
\r
2006 embeddedMenu.setLayout(flowLayout1);
\r
2007 embeddedEdit.setText("Edit");
\r
2008 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2009 embeddedSearch.setText("Search");
\r
2010 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2011 embeddedView.setText("View");
\r
2012 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2013 embeddedColour.setText("Colour");
\r
2014 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2015 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2016 embeddedFile.setText("File");
\r
2017 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2018 embeddedHelp.setText("Help");
\r
2019 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2020 embeddedCalculate.setText("Calculate");
\r
2021 embeddedMenu.add(embeddedFile);
\r
2022 embeddedMenu.add(embeddedEdit);
\r
2023 embeddedMenu.add(embeddedSearch);
\r
2024 embeddedMenu.add(embeddedView);
\r
2025 embeddedMenu.add(embeddedColour);
\r
2026 embeddedMenu.add(embeddedCalculate);
\r
2027 embeddedMenu.add(embeddedHelp);
\r
2028 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2029 flowLayout1.setHgap(2);
\r
2030 flowLayout1.setVgap(0);
\r
2031 embeddedFile.addMouseListener(this);
\r
2032 embeddedEdit.addMouseListener(this);
\r
2033 embeddedSearch.addMouseListener(this);
\r
2034 embeddedView.addMouseListener(this);
\r
2035 embeddedColour.addMouseListener(this);
\r
2036 embeddedCalculate.addMouseListener(this);
\r
2037 embeddedHelp.addMouseListener(this);
\r
2039 setVisible(false);
\r
2040 fileMenu.remove(closeMenuItem);
\r
2041 fileMenu.remove(2); // Seperator
\r
2043 applet.setLayout(new BorderLayout());
\r
2044 applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2045 applet.add(statusBar, BorderLayout.SOUTH);
\r
2046 applet.validate();
\r
2049 alignPanel.setSize(applet.size().width, applet.size().height
\r
2050 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2052 applet.add(alignPanel, BorderLayout.CENTER);
\r
2053 applet.validate();
\r
2058 PopupMenu filePopup, editPopup, searchPopup,
\r
2059 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2061 public void mousePressed(MouseEvent evt)
\r
2063 PopupMenu popup = null;
\r
2064 Label source = (Label)evt.getSource();
\r
2065 if(source==embeddedFile)
\r
2067 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2069 else if(source==embeddedEdit)
\r
2071 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2073 else if(source==embeddedSearch)
\r
2075 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2077 else if(source==embeddedView)
\r
2079 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2081 else if(source==embeddedColour)
\r
2083 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2085 else if(source==embeddedCalculate)
\r
2087 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2089 else if(source==embeddedHelp)
\r
2091 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2094 embeddedMenu.add(popup);
\r
2095 popup.show(embeddedMenu,
\r
2096 source.getBounds().x,
\r
2097 source.getBounds().y + source.getBounds().getSize().height);
\r
2100 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2106 popup = new PopupMenu();
\r
2107 int m, mSize = original.getItemCount();
\r
2108 for(m=0; m<mSize; m++)
\r
2110 popup.add(original.getItem(m));
\r
2117 public void mouseClicked(MouseEvent evt)
\r
2119 public void mouseReleased(MouseEvent evt)
\r
2121 public void mouseEntered(MouseEvent evt)
\r
2123 public void mouseExited(MouseEvent evt)
\r