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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206 viewMenu.addSeparator();
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207 viewMenu.add(sequenceFeatures);
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208 viewMenu.add(featureSettings);
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211 alignPanel.repaint();
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214 catch (Exception ex)
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216 System.out.println("Error parsing groups file: " + ex);
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220 public void keyPressed(KeyEvent evt)
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222 switch (evt.getKeyCode())
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224 case 27: // escape key
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225 deselectAllSequenceMenuItem_actionPerformed();
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227 case KeyEvent.VK_X:
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228 if (evt.isControlDown() || evt.isMetaDown())
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230 cut_actionPerformed();
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233 case KeyEvent.VK_C:
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234 if (evt.isControlDown() || evt.isMetaDown())
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236 copy_actionPerformed();
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239 case KeyEvent.VK_V:
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240 if (evt.isControlDown() || evt.isMetaDown())
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245 case KeyEvent.VK_A:
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246 if (evt.isControlDown() || evt.isMetaDown())
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248 selectAllSequenceMenuItem_actionPerformed();
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251 case KeyEvent.VK_DOWN:
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252 moveSelectedSequences(false);
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254 case KeyEvent.VK_UP:
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255 moveSelectedSequences(true);
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257 case KeyEvent.VK_F:
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258 if (evt.isControlDown())
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260 findMenuItem_actionPerformed();
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263 case KeyEvent.VK_BACK_SPACE:
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264 case KeyEvent.VK_DELETE:
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265 cut_actionPerformed();
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269 public void keyReleased(KeyEvent evt)
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271 public void keyTyped(KeyEvent evt)
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274 public void itemStateChanged(ItemEvent evt)
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276 if(evt.getSource()==colourTextMenuItem)
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277 colourTextMenuItem_actionPerformed();
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278 else if(evt.getSource()==wrapMenuItem)
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279 wrapMenuItem_actionPerformed();
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280 else if(evt.getSource()==scaleAbove)
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281 scaleAbove_actionPerformed();
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282 else if(evt.getSource()==scaleLeft)
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283 scaleLeft_actionPerformed();
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284 else if(evt.getSource()==scaleRight)
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285 scaleRight_actionPerformed();
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286 else if(evt.getSource()==seqLimits)
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287 seqLimits_itemStateChanged();
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288 else if(evt.getSource()==viewBoxesMenuItem)
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289 viewBoxesMenuItem_actionPerformed();
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290 else if(evt.getSource()==viewTextMenuItem)
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291 viewTextMenuItem_actionPerformed();
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292 else if(evt.getSource()==renderGapsMenuItem)
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293 renderGapsMenuItem_actionPerformed();
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294 else if(evt.getSource()==annotationPanelMenuItem)
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295 annotationPanelMenuItem_actionPerformed();
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296 else if(evt.getSource()==sequenceFeatures)
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297 { viewport.showSequenceFeatures(sequenceFeatures.getState());
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298 alignPanel.seqPanel.seqCanvas.repaint();
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300 else if(evt.getSource()==conservationMenuItem)
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301 conservationMenuItem_actionPerformed();
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302 else if(evt.getSource()==abovePIDThreshold)
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303 abovePIDThreshold_actionPerformed();
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304 else if(evt.getSource()==applyToAllGroups)
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305 applyToAllGroups_actionPerformed();
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307 public void actionPerformed(ActionEvent evt)
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309 if(evt.getSource()==inputText)
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310 inputText_actionPerformed();
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311 else if(evt.getSource()==closeMenuItem)
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312 closeMenuItem_actionPerformed();
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313 else if(evt.getSource()==copy)
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314 copy_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()==inputText)
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320 inputText_actionPerformed();
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321 else if(evt.getSource()==closeMenuItem)
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322 closeMenuItem_actionPerformed();
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323 else if(evt.getSource()==undoMenuItem)
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324 undoMenuItem_actionPerformed();
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325 else if(evt.getSource()==redoMenuItem)
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326 redoMenuItem_actionPerformed();
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327 else if(evt.getSource()==copy)
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328 copy_actionPerformed();
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329 else if(evt.getSource()==pasteNew)
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330 pasteNew_actionPerformed();
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331 else if(evt.getSource()==pasteThis)
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332 pasteThis_actionPerformed();
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333 else if(evt.getSource()==cut)
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334 cut_actionPerformed();
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335 else if(evt.getSource()==delete)
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336 delete_actionPerformed();
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337 else if(evt.getSource()==deleteGroups)
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338 deleteGroups_actionPerformed();
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339 else if(evt.getSource()==selectAllSequenceMenuItem)
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340 selectAllSequenceMenuItem_actionPerformed();
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341 else if(evt.getSource()==deselectAllSequenceMenuItem)
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342 deselectAllSequenceMenuItem_actionPerformed();
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343 else if(evt.getSource()==invertSequenceMenuItem)
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344 invertSequenceMenuItem_actionPerformed();
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345 else if(evt.getSource()==remove2LeftMenuItem)
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346 remove2LeftMenuItem_actionPerformed();
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347 else if(evt.getSource()==remove2RightMenuItem)
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348 remove2RightMenuItem_actionPerformed();
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349 else if(evt.getSource()==removeGappedColumnMenuItem)
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350 removeGappedColumnMenuItem_actionPerformed();
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351 else if(evt.getSource()==removeAllGapsMenuItem)
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352 removeAllGapsMenuItem_actionPerformed();
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353 else if(evt.getSource()==findMenuItem)
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354 findMenuItem_actionPerformed();
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355 else if(evt.getSource()==font)
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356 font_actionPerformed();
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357 else if(evt.getSource()==featureSettings)
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358 featureSettings_actionPerformed();
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359 else if(evt.getSource()==overviewMenuItem)
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360 overviewMenuItem_actionPerformed();
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361 else if(evt.getSource()==noColourmenuItem)
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362 noColourmenuItem_actionPerformed();
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363 else if(evt.getSource()==clustalColour)
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364 clustalColour_actionPerformed();
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365 else if(evt.getSource()==zappoColour)
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366 zappoColour_actionPerformed();
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367 else if(evt.getSource()==taylorColour)
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368 taylorColour_actionPerformed();
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369 else if(evt.getSource()==hydrophobicityColour)
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370 hydrophobicityColour_actionPerformed();
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371 else if(evt.getSource()==helixColour)
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372 helixColour_actionPerformed();
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373 else if(evt.getSource()==strandColour)
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374 strandColour_actionPerformed();
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375 else if(evt.getSource()==turnColour)
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376 turnColour_actionPerformed();
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377 else if(evt.getSource()==buriedColour)
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378 buriedColour_actionPerformed();
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379 else if(evt.getSource()==nucleotideColour)
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380 nucleotideColour_actionPerformed();
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381 else if(evt.getSource()==modifyPID)
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382 modifyPID_actionPerformed();
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383 else if(evt.getSource()==modifyConservation)
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384 modifyConservation_actionPerformed();
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385 else if(evt.getSource()==userDefinedColour)
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386 userDefinedColour_actionPerformed();
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387 else if(evt.getSource()==PIDColour)
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388 PIDColour_actionPerformed();
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389 else if(evt.getSource()==BLOSUM62Colour)
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390 BLOSUM62Colour_actionPerformed();
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391 else if(evt.getSource()==sortPairwiseMenuItem)
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392 sortPairwiseMenuItem_actionPerformed();
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393 else if(evt.getSource()==sortIDMenuItem)
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394 sortIDMenuItem_actionPerformed();
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395 else if(evt.getSource()==sortGroupMenuItem)
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396 sortGroupMenuItem_actionPerformed();
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397 else if(evt.getSource()==removeRedundancyMenuItem)
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398 removeRedundancyMenuItem_actionPerformed();
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399 else if(evt.getSource()==pairwiseAlignmentMenuItem)
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400 pairwiseAlignmentMenuItem_actionPerformed();
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401 else if(evt.getSource()==PCAMenuItem)
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402 PCAMenuItem_actionPerformed();
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403 else if(evt.getSource()==averageDistanceTreeMenuItem)
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404 averageDistanceTreeMenuItem_actionPerformed();
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405 else if(evt.getSource()==neighbourTreeMenuItem)
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406 neighbourTreeMenuItem_actionPerformed();
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407 else if(evt.getSource()==njTreeBlosumMenuItem)
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408 njTreeBlosumMenuItem_actionPerformed();
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409 else if(evt.getSource()==avDistanceTreeBlosumMenuItem)
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410 avTreeBlosumMenuItem_actionPerformed();
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411 else if(evt.getSource()==documentation)
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412 documentation_actionPerformed();
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413 else if(evt.getSource()==about)
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414 about_actionPerformed();
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418 public void inputText_actionPerformed()
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420 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
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421 Frame frame = new Frame();
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423 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
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426 protected void outputText_actionPerformed(ActionEvent e)
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428 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
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429 Frame frame = new Frame();
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431 jalview.bin.JalviewLite.addFrame(frame,
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432 "Alignment output - " + e.getActionCommand(),
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434 cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
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435 viewport.getAlignment().getSequences(),
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436 viewport.showJVSuffix));
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439 public void closeMenuItem_actionPerformed()
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441 PaintRefresher.components.remove(viewport.alignment);
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442 if(PaintRefresher.components.size()==0 && applet==null)
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448 Stack historyList = new Stack();
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449 Stack redoList = new Stack();
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451 void updateEditMenuBar()
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453 if (historyList.size() > 0)
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455 undoMenuItem.setEnabled(true);
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456 HistoryItem hi = (HistoryItem) historyList.peek();
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457 undoMenuItem.setLabel("Undo " + hi.getDescription());
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461 undoMenuItem.setEnabled(false);
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462 undoMenuItem.setLabel("Undo");
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465 if (redoList.size() > 0)
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467 redoMenuItem.setEnabled(true);
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468 HistoryItem hi = (HistoryItem) redoList.peek();
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469 redoMenuItem.setLabel("Redo " + hi.getDescription());
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473 redoMenuItem.setEnabled(false);
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474 redoMenuItem.setLabel("Redo");
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478 public void addHistoryItem(HistoryItem hi)
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480 historyList.push(hi);
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481 updateEditMenuBar();
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484 protected void undoMenuItem_actionPerformed()
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486 HistoryItem hi = (HistoryItem) historyList.pop();
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487 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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488 HistoryItem.HIDE));
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489 restoreHistoryItem(hi);
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490 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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493 protected void redoMenuItem_actionPerformed()
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495 HistoryItem hi = (HistoryItem) redoList.pop();
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496 restoreHistoryItem(hi);
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497 updateEditMenuBar();
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498 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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501 // used by undo and redo
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502 void restoreHistoryItem(HistoryItem hi)
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504 if (hi.getType() == HistoryItem.SORT)
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506 for (int i = 0; i < hi.getSequences().size(); i++)
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508 viewport.alignment.getSequences().setElementAt(hi.getSequences().
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514 for (int i = 0; i < hi.getSequences().size(); i++)
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516 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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517 if (restore.getLength() == 0)
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519 // log.System.out.println(hi.getHidden().elementAt(i));
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520 restore.setSequence(hi.getHidden().elementAt(i).toString());
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521 viewport.alignment.getSequences().insertElementAt(
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523 hi.getAlignIndex(i));
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527 restore.setSequence(hi.getHidden().elementAt(i).toString());
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530 if (hi.getType() == HistoryItem.PASTE)
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532 for (int i = viewport.alignment.getHeight() - 1;
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533 i > hi.getSequences().size() - 1; i--)
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535 viewport.alignment.deleteSequence(i);
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540 updateEditMenuBar();
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542 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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545 public void moveSelectedSequences(boolean up)
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547 SequenceGroup sg = viewport.getSelectionGroup();
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555 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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557 SequenceI seq = viewport.alignment.getSequenceAt(i);
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558 if (!sg.sequences.contains(seq))
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563 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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564 if (sg.sequences.contains(temp))
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569 viewport.alignment.getSequences().setElementAt(temp, i);
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570 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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575 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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577 SequenceI seq = viewport.alignment.getSequenceAt(i);
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578 if (!sg.sequences.contains(seq))
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583 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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584 if (sg.sequences.contains(temp))
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589 viewport.alignment.getSequences().setElementAt(temp, i);
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590 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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594 alignPanel.repaint();
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597 StringBuffer copiedSequences;
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598 protected void copy_actionPerformed()
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600 if (viewport.getSelectionGroup() == null)
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605 SequenceGroup sg = viewport.getSelectionGroup();
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606 copiedSequences = new StringBuffer();
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607 Hashtable orderedSeqs = new Hashtable();
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608 for (int i = 0; i < sg.getSize(); i++)
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610 SequenceI seq = sg.getSequenceAt(i);
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611 int index = viewport.alignment.findIndex(seq);
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612 orderedSeqs.put(index + "", seq);
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615 int index = 0, startRes, endRes;
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618 for (int i = 0; i < sg.getSize(); i++)
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620 SequenceI seq = null;
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622 while (seq == null)
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624 if (orderedSeqs.containsKey(index + ""))
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626 seq = (SequenceI) orderedSeqs.get(index + "");
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638 //Returns residue following index if gap
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639 startRes = seq.findPosition(sg.getStartRes());
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642 //Need to find the residue preceeding index if gap
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645 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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647 ch = seq.getCharAt(j);
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648 if (!jalview.util.Comparison.isGap( (ch)))
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656 endRes += seq.getStart() -1;
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659 copiedSequences.append(seq.getName() + "\t" +
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662 seq.getSequence(sg.getStartRes(),
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663 sg.getEndRes() + 1) + "\n");
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668 protected void pasteNew_actionPerformed()
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673 protected void pasteThis_actionPerformed()
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675 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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676 HistoryItem.PASTE));
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680 void paste(boolean newAlignment)
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684 if (copiedSequences == null)
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689 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
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690 Vector seqs = new Vector();
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691 while (st.hasMoreElements())
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693 String name = st.nextToken();
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694 int start = Integer.parseInt(st.nextToken());
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695 int end = Integer.parseInt(st.nextToken());
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696 Sequence sequence = new Sequence(name, st.nextToken(), start, end);
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700 viewport.alignment.addSequence(sequence);
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704 seqs.addElement(sequence);
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710 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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711 for (int i = 0; i < seqs.size(); i++)
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713 newSeqs[i] = (SequenceI) seqs.elementAt(i);
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716 String newtitle = new String("Copied sequences");
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717 if (getTitle().startsWith("Copied sequences"))
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719 newtitle = getTitle();
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723 newtitle = newtitle.concat("- from " + getTitle());
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725 AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);
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727 jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
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728 NEW_WINDOW_HEIGHT);
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732 viewport.setEndSeq(viewport.alignment.getHeight());
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733 viewport.alignment.getWidth();
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734 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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738 catch (Exception ex)
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739 {} // could be anything being pasted in here
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743 protected void cut_actionPerformed()
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745 copy_actionPerformed();
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746 delete_actionPerformed();
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749 protected void delete_actionPerformed()
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751 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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752 HistoryItem.HIDE));
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753 if (viewport.getSelectionGroup() == null)
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759 SequenceGroup sg = viewport.getSelectionGroup();
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760 boolean allSequences = false;
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761 if(sg.sequences.size()==viewport.alignment.getHeight())
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762 allSequences = true;
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764 for (int i = 0; i < sg.sequences.size(); i++)
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766 SequenceI seq = sg.getSequenceAt(i);
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767 int index = viewport.getAlignment().findIndex(seq);
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768 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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770 // If the cut affects all sequences, remove highlighted columns
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773 viewport.getColumnSelection().removeElements(sg.getStartRes(),
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774 sg.getEndRes() + 1);
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778 if (seq.getSequence().length() < 1)
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780 viewport.getAlignment().deleteSequence(seq);
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784 viewport.getAlignment().getSequences().setElementAt(seq, index);
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788 viewport.setSelectionGroup(null);
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789 viewport.alignment.deleteGroup(sg);
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790 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
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791 if (viewport.getAlignment().getHeight() < 1)
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795 this.setVisible(false);
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797 catch (Exception ex)
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800 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
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804 protected void deleteGroups_actionPerformed()
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806 viewport.alignment.deleteAllGroups();
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807 viewport.setSelectionGroup(null);
\r
809 alignPanel.repaint();
\r
812 public void selectAllSequenceMenuItem_actionPerformed()
\r
814 SequenceGroup sg = new SequenceGroup();
\r
815 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
817 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
\r
819 sg.setEndRes(viewport.alignment.getWidth()-1);
\r
820 viewport.setSelectionGroup(sg);
\r
821 alignPanel.repaint();
\r
822 PaintRefresher.Refresh(null, viewport.alignment);
\r
825 public void deselectAllSequenceMenuItem_actionPerformed()
\r
827 viewport.setSelectionGroup(null);
\r
828 viewport.getColumnSelection().clear();
\r
829 viewport.setSelectionGroup(null);
\r
830 alignPanel.idPanel.idCanvas.searchResults = null;
\r
831 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
\r
832 alignPanel.repaint();
\r
833 PaintRefresher.Refresh(null, viewport.alignment);
\r
836 public void invertSequenceMenuItem_actionPerformed()
\r
838 SequenceGroup sg = viewport.getSelectionGroup();
\r
839 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
\r
841 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
\r
844 PaintRefresher.Refresh(null, viewport.alignment);
\r
847 public void remove2LeftMenuItem_actionPerformed()
\r
849 ColumnSelection colSel = viewport.getColumnSelection();
\r
850 if (colSel.size() > 0)
\r
852 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
\r
853 HistoryItem.HIDE));
\r
854 int min = colSel.getMin();
\r
855 viewport.getAlignment().trimLeft(min);
\r
856 colSel.compensateForEdit(0, min);
\r
858 if (viewport.getSelectionGroup() != null)
\r
860 viewport.getSelectionGroup().adjustForRemoveLeft(min);
\r
863 Vector groups = viewport.alignment.getGroups();
\r
864 for (int i = 0; i < groups.size(); i++)
\r
866 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
867 if (!sg.adjustForRemoveLeft(min))
\r
869 viewport.alignment.deleteGroup(sg);
\r
872 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
876 public void remove2RightMenuItem_actionPerformed()
\r
878 ColumnSelection colSel = viewport.getColumnSelection();
\r
879 if (colSel.size() > 0)
\r
881 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
\r
882 HistoryItem.HIDE));
\r
883 int max = colSel.getMax();
\r
884 viewport.getAlignment().trimRight(max);
\r
885 if (viewport.getSelectionGroup() != null)
\r
887 viewport.getSelectionGroup().adjustForRemoveRight(max);
\r
890 Vector groups = viewport.alignment.getGroups();
\r
891 for (int i = 0; i < groups.size(); i++)
\r
893 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
894 if (!sg.adjustForRemoveRight(max))
\r
896 viewport.alignment.deleteGroup(sg);
\r
899 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
904 public void removeGappedColumnMenuItem_actionPerformed()
\r
906 addHistoryItem(new HistoryItem("Remove Gapped Columns",
\r
907 viewport.alignment,
\r
908 HistoryItem.HIDE));
\r
910 //This is to maintain viewport position on first residue
\r
911 //of first sequence
\r
912 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
913 int startRes = seq.findPosition(viewport.startRes);
\r
915 viewport.getAlignment().removeGaps();
\r
917 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
919 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
922 public void removeAllGapsMenuItem_actionPerformed()
\r
924 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
\r
925 HistoryItem.HIDE));
\r
927 //This is to maintain viewport position on first residue
\r
928 //of first sequence
\r
929 SequenceI seq = viewport.alignment.getSequenceAt(0);
\r
930 int startRes = seq.findPosition(viewport.startRes);
\r
937 int start=0, end = viewport.alignment.getWidth();
\r
939 if (viewport.getSelectionGroup() != null
\r
940 && viewport.getSelectionGroup().sequences != null
\r
941 && viewport.getSelectionGroup().sequences.size()>0)
\r
943 seqs = viewport.getSelectionGroup().sequences;
\r
944 start = viewport.getSelectionGroup().getStartRes();
\r
945 end = viewport.getSelectionGroup().getEndRes()+1;
\r
948 seqs = viewport.alignment.getSequences();
\r
950 for (int i = 0; i < seqs.size(); i++)
\r
952 current = (SequenceI) seqs.elementAt(i);
\r
953 jSize = current.getLength();
\r
955 // Removing a range is much quicker than removing gaps
\r
956 // one by one for long sequences
\r
958 int rangeStart=-1, rangeEnd=-1;
\r
962 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
\r
979 current.deleteChars(rangeStart, rangeEnd);
\r
980 j-=rangeEnd-rangeStart;
\r
981 jSize-=rangeEnd-rangeStart;
\r
989 while (j < end && j < jSize);
\r
992 current.deleteChars(rangeStart, rangeEnd);
\r
995 viewport.setStartRes(seq.findIndex(startRes)-1);
\r
996 viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
\r
999 public void alignmentChanged()
\r
1001 viewport.updateConsensus();
\r
1002 viewport.updateConservation ();
\r
1003 resetAllColourSchemes();
\r
1004 if(alignPanel.overviewPanel!=null)
\r
1005 alignPanel.overviewPanel.updateOverviewImage();
\r
1007 viewport.alignment.adjustSequenceAnnotations();
\r
1008 alignPanel.repaint();
\r
1011 void resetAllColourSchemes()
\r
1013 ColourSchemeI cs = viewport.globalColourScheme;
\r
1016 if (cs instanceof ClustalxColourScheme)
\r
1018 ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
\r
1019 resetClustalX(viewport.alignment.getSequences(),
\r
1020 viewport.alignment.getWidth());
\r
1023 cs.setConsensus(viewport.vconsensus);
\r
1024 if (cs.conservationApplied())
\r
1026 Alignment al = (Alignment) viewport.alignment;
\r
1027 Conservation c = new Conservation("All",
\r
1028 ResidueProperties.propHash, 3,
\r
1029 al.getSequences(), 0,
\r
1030 al.getWidth() - 1);
\r
1032 c.verdict(false, viewport.ConsPercGaps);
\r
1034 cs.setConservation(c);
\r
1038 int s, sSize = viewport.alignment.getGroups().size();
\r
1039 for(s=0; s<sSize; s++)
\r
1041 SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
\r
1042 if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
\r
1044 ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
\r
1046 sg.recalcConservation();
\r
1052 public void findMenuItem_actionPerformed()
\r
1054 new Finder(alignPanel);
\r
1057 public void font_actionPerformed()
\r
1059 new FontChooser(alignPanel);
\r
1063 public void seqLimits_itemStateChanged()
\r
1065 viewport.setShowJVSuffix(seqLimits.getState());
\r
1066 alignPanel.fontChanged();
\r
1067 alignPanel.repaint();
\r
1071 protected void colourTextMenuItem_actionPerformed()
\r
1073 viewport.setColourText(colourTextMenuItem.getState());
\r
1074 alignPanel.repaint();
\r
1077 protected void wrapMenuItem_actionPerformed()
\r
1079 viewport.setWrapAlignment(wrapMenuItem.getState());
\r
1080 alignPanel.setWrapAlignment(wrapMenuItem.getState());
\r
1081 scaleAbove.setEnabled(wrapMenuItem.getState());
\r
1082 scaleLeft.setEnabled(wrapMenuItem.getState());
\r
1083 scaleRight.setEnabled(wrapMenuItem.getState());
\r
1084 alignPanel.repaint();
\r
1087 protected void scaleAbove_actionPerformed()
\r
1089 viewport.setScaleAboveWrapped(scaleAbove.getState());
\r
1090 alignPanel.repaint();
\r
1093 protected void scaleLeft_actionPerformed()
\r
1095 viewport.setScaleLeftWrapped(scaleLeft.getState());
\r
1096 alignPanel.repaint();
\r
1099 protected void scaleRight_actionPerformed()
\r
1101 viewport.setScaleRightWrapped(scaleRight.getState());
\r
1102 alignPanel.repaint();
\r
1105 public void viewBoxesMenuItem_actionPerformed()
\r
1107 viewport.setShowBoxes(viewBoxesMenuItem.getState());
\r
1108 alignPanel.repaint();
\r
1111 public void viewTextMenuItem_actionPerformed()
\r
1113 viewport.setShowText(viewTextMenuItem.getState());
\r
1114 alignPanel.repaint();
\r
1117 protected void renderGapsMenuItem_actionPerformed()
\r
1119 viewport.setRenderGaps(renderGapsMenuItem.getState());
\r
1120 alignPanel.repaint();
\r
1123 public void annotationPanelMenuItem_actionPerformed()
\r
1125 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
\r
1126 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
\r
1129 public void featureSettings_actionPerformed()
\r
1131 new FeatureSettings(viewport, alignPanel);
\r
1134 public void overviewMenuItem_actionPerformed()
\r
1136 if (alignPanel.overviewPanel != null)
\r
1141 Frame frame = new Frame();
\r
1142 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1143 frame.add(overview);
\r
1144 // +50 must allow for applet frame window
\r
1145 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
\r
1146 overview.preferredSize().width,
\r
1147 overview.preferredSize().height + 50);
\r
1150 frame.addWindowListener(new WindowAdapter()
\r
1152 public void windowClosing(WindowEvent e)
\r
1154 alignPanel.setOverviewPanel(null);
\r
1158 alignPanel.setOverviewPanel(overview);
\r
1162 protected void noColourmenuItem_actionPerformed()
\r
1164 changeColour(null);
\r
1167 public void clustalColour_actionPerformed()
\r
1169 abovePIDThreshold.setState(false);
\r
1170 changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
\r
1171 viewport.alignment.getWidth()));
\r
1174 public void zappoColour_actionPerformed()
\r
1176 changeColour(new ZappoColourScheme());
\r
1179 public void taylorColour_actionPerformed()
\r
1181 changeColour(new TaylorColourScheme());
\r
1184 public void hydrophobicityColour_actionPerformed()
\r
1186 changeColour(new HydrophobicColourScheme());
\r
1189 public void helixColour_actionPerformed()
\r
1191 changeColour(new HelixColourScheme());
\r
1194 public void strandColour_actionPerformed()
\r
1196 changeColour(new StrandColourScheme());
\r
1199 public void turnColour_actionPerformed()
\r
1201 changeColour(new TurnColourScheme());
\r
1204 public void buriedColour_actionPerformed()
\r
1206 changeColour(new BuriedColourScheme());
\r
1209 public void nucleotideColour_actionPerformed()
\r
1211 changeColour(new NucleotideColourScheme());
\r
1214 protected void applyToAllGroups_actionPerformed()
\r
1216 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
\r
1219 void changeColour(ColourSchemeI cs)
\r
1221 int threshold = 0;
\r
1225 if (viewport.getAbovePIDThreshold())
\r
1227 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
\r
1229 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1231 viewport.setGlobalColourScheme(cs);
\r
1235 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1238 if (viewport.getConservationSelected())
\r
1241 Alignment al = (Alignment) viewport.alignment;
\r
1242 Conservation c = new Conservation("All",
\r
1243 ResidueProperties.propHash, 3,
\r
1244 al.getSequences(), 0,
\r
1245 al.getWidth() - 1);
\r
1248 c.verdict(false, viewport.ConsPercGaps);
\r
1250 cs.setConservation(c);
\r
1252 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
\r
1258 cs.setConservation(null);
\r
1261 cs.setConsensus(viewport.vconsensus);
\r
1264 viewport.setGlobalColourScheme(cs);
\r
1266 if (viewport.getColourAppliesToAllGroups())
\r
1268 Vector groups = viewport.alignment.getGroups();
\r
1269 for (int i = 0; i < groups.size(); i++)
\r
1271 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1278 if (cs instanceof ClustalxColourScheme)
\r
1280 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1286 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1288 catch (Exception ex)
\r
1290 ex.printStackTrace();
\r
1295 if (viewport.getAbovePIDThreshold()
\r
1296 || cs instanceof PIDColourScheme
\r
1297 || cs instanceof Blosum62ColourScheme)
\r
1299 sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1300 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
\r
1303 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1305 if (viewport.getConservationSelected())
\r
1307 Conservation c = new Conservation("Group",
\r
1308 ResidueProperties.propHash, 3,
\r
1310 viewport.alignment.getWidth() - 1);
\r
1312 c.verdict(false, viewport.ConsPercGaps);
\r
1313 sg.cs.setConservation(c);
\r
1317 sg.cs.setConservation(null);
\r
1318 sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1325 if (alignPanel.getOverviewPanel() != null)
\r
1327 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1330 alignPanel.repaint();
\r
1335 protected void modifyPID_actionPerformed()
\r
1337 if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
\r
1339 SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
\r
1341 SliderPanel.showPIDSlider();
\r
1345 protected void modifyConservation_actionPerformed()
\r
1347 if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
\r
1349 SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
\r
1351 SliderPanel.showConservationSlider();
\r
1355 protected void conservationMenuItem_actionPerformed()
\r
1357 viewport.setConservationSelected(conservationMenuItem.getState());
\r
1359 viewport.setAbovePIDThreshold(false);
\r
1360 abovePIDThreshold.setState(false);
\r
1362 changeColour(viewport.getGlobalColourScheme());
\r
1364 modifyConservation_actionPerformed();
\r
1367 public void abovePIDThreshold_actionPerformed()
\r
1369 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
\r
1371 conservationMenuItem.setState(false);
\r
1372 viewport.setConservationSelected(false);
\r
1374 changeColour(viewport.getGlobalColourScheme());
\r
1376 modifyPID_actionPerformed();
\r
1379 public void userDefinedColour_actionPerformed()
\r
1381 new UserDefinedColours(alignPanel, null);
\r
1384 public void PIDColour_actionPerformed()
\r
1386 changeColour(new PIDColourScheme());
\r
1389 public void BLOSUM62Colour_actionPerformed()
\r
1391 changeColour(new Blosum62ColourScheme());
\r
1394 public void sortPairwiseMenuItem_actionPerformed()
\r
1396 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1397 HistoryItem.SORT));
\r
1398 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1399 viewport.getAlignment().getSequenceAt(0));
\r
1400 alignPanel.repaint();
\r
1403 public void sortIDMenuItem_actionPerformed()
\r
1405 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1406 HistoryItem.SORT));
\r
1407 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1408 alignPanel.repaint();
\r
1411 public void sortGroupMenuItem_actionPerformed()
\r
1413 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1414 HistoryItem.SORT));
\r
1415 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1416 alignPanel.repaint();
\r
1420 public void removeRedundancyMenuItem_actionPerformed()
\r
1422 RedundancyPanel sp = new RedundancyPanel(alignPanel);
\r
1423 Frame frame = new Frame();
\r
1425 jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",
\r
1430 public void pairwiseAlignmentMenuItem_actionPerformed()
\r
1432 if (viewport.getSelectionGroup().getSize() > 1)
\r
1434 Frame frame = new Frame();
\r
1435 frame.add(new PairwiseAlignPanel(alignPanel));
\r
1436 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
\r
1440 public void PCAMenuItem_actionPerformed()
\r
1442 //are the sequences aligned?
\r
1443 if (!viewport.alignment.isAligned())
\r
1445 SequenceI current;
\r
1446 int Width = viewport.getAlignment().getWidth();
\r
1448 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1451 current = viewport.getAlignment().getSequenceAt(i);
\r
1453 if (current.getLength() < Width)
\r
1455 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1458 alignPanel.repaint();
\r
1461 if ( (viewport.getSelectionGroup() != null &&
\r
1462 viewport.getSelectionGroup().getSize() < 4 &&
\r
1463 viewport.getSelectionGroup().getSize() > 0)
\r
1464 || viewport.getAlignment().getHeight() < 4)
\r
1471 new PCAPanel(viewport);
\r
1473 catch (java.lang.OutOfMemoryError ex)
\r
1479 public void averageDistanceTreeMenuItem_actionPerformed()
\r
1481 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1484 public void neighbourTreeMenuItem_actionPerformed()
\r
1486 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1489 protected void njTreeBlosumMenuItem_actionPerformed()
\r
1491 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1494 protected void avTreeBlosumMenuItem_actionPerformed()
\r
1496 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
\r
1499 void NewTreePanel(String type, String pwType, String title)
\r
1501 //are the sequences aligned?
\r
1502 if (!viewport.alignment.isAligned())
\r
1504 SequenceI current;
\r
1505 int Width = viewport.getAlignment().getWidth();
\r
1507 for (int i = 0; i < viewport.getAlignment().getSequences().size();
\r
1510 current = viewport.getAlignment().getSequenceAt(i);
\r
1512 if (current.getLength() < Width)
\r
1514 current.insertCharAt(Width - 1, viewport.getGapCharacter());
\r
1517 alignPanel.repaint();
\r
1521 final TreePanel tp;
\r
1522 if (viewport.getSelectionGroup() != null &&
\r
1523 viewport.getSelectionGroup().getSize() > 3)
\r
1525 tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
\r
1527 0, viewport.alignment.getWidth());
\r
1531 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
\r
1532 type, pwType, 0, viewport.alignment.getWidth());
\r
1535 addTreeMenuItem(tp, title);
\r
1537 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
\r
1540 public void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1542 final MenuItem item = new MenuItem(title);
\r
1543 sortByTreeMenu.add(item);
\r
1544 item.addActionListener(new java.awt.event.ActionListener()
\r
1546 public void actionPerformed(ActionEvent evt)
\r
1548 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1549 HistoryItem.SORT));
\r
1550 AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
\r
1551 alignPanel.repaint();
\r
1555 treePanel.addWindowListener(new WindowAdapter()
\r
1557 public void windowClosing(WindowEvent e)
\r
1559 sortByTreeMenu.remove(item);
\r
1564 protected void documentation_actionPerformed()
\r
1566 showURL("http://www.jalview.org/help.html", "HELP");
\r
1569 protected void about_actionPerformed()
\r
1572 class AboutPanel extends Canvas
\r
1575 public AboutPanel(String version)
\r
1576 { this.version = version; }
\r
1578 public void paint(Graphics g)
\r
1580 g.setColor(Color.white);
\r
1581 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1582 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1583 FontMetrics fm = g.getFontMetrics();
\r
1584 int fh = fm.getHeight();
\r
1586 g.setColor(Color.black);
\r
1587 g.setFont(new Font("Helvetica", Font.BOLD, 14));
\r
1588 g.drawString("Jalview - Release "+version, 200, y += fh);
\r
1589 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
\r
1590 g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
\r
1592 g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
\r
1595 "For any issues relating to Jalview, email help@jalview.org", x,
\r
1597 g.drawString("If you use JalView, please cite:", x, y += fh + 8);
\r
1598 g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
\r
1600 g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);
\r
1604 String version = "test";
\r
1605 java.net.URL url = getClass().getResource("/.build_properties");
\r
1610 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1611 url.openStream()));
\r
1613 while ( (line = reader.readLine()) != null)
\r
1615 if (line.indexOf("VERSION") > -1)
\r
1617 version = line.substring(line.indexOf("=") + 1);
\r
1621 catch (Exception ex)
\r
1623 ex.printStackTrace();
\r
1628 Frame frame = new Frame();
\r
1629 frame.add(new AboutPanel(version));
\r
1630 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
\r
1634 public void showURL(String url, String target)
\r
1636 if (applet == null)
\r
1638 System.out.println("Not running as applet - no browser available.");
\r
1644 applet.getAppletContext().showDocument(new java.net.URL(url),
\r
1647 catch (Exception ex)
\r
1649 ex.printStackTrace();
\r
1655 //////////////////////////////////////////////////////////////////////////////////
\r
1656 //JBuilder Graphics here
\r
1658 protected MenuBar alignFrameMenuBar = new MenuBar();
\r
1659 protected Menu fileMenu = new Menu();
\r
1660 protected MenuItem closeMenuItem = new MenuItem();
\r
1661 protected Menu editMenu = new Menu();
\r
1662 protected Menu viewMenu = new Menu();
\r
1663 protected Menu colourMenu = new Menu();
\r
1664 protected Menu calculateMenu = new Menu();
\r
1665 protected MenuItem selectAllSequenceMenuItem = new MenuItem();
\r
1666 protected MenuItem deselectAllSequenceMenuItem = new MenuItem();
\r
1667 protected MenuItem invertSequenceMenuItem = new MenuItem();
\r
1668 protected MenuItem remove2LeftMenuItem = new MenuItem();
\r
1669 protected MenuItem remove2RightMenuItem = new MenuItem();
\r
1670 protected MenuItem removeGappedColumnMenuItem = new MenuItem();
\r
1671 protected MenuItem removeAllGapsMenuItem = new MenuItem();
\r
1672 protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
\r
1673 protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
\r
1674 protected MenuItem sortPairwiseMenuItem = new MenuItem();
\r
1675 protected MenuItem sortIDMenuItem = new MenuItem();
\r
1676 protected MenuItem sortGroupMenuItem = new MenuItem();
\r
1677 protected MenuItem removeRedundancyMenuItem = new MenuItem();
\r
1678 protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
\r
1679 protected MenuItem PCAMenuItem = new MenuItem();
\r
1680 protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
\r
1681 protected MenuItem neighbourTreeMenuItem = new MenuItem();
\r
1682 BorderLayout borderLayout1 = new BorderLayout();
\r
1683 public Label statusBar = new Label();
\r
1684 protected Menu outputTextboxMenu = new Menu();
\r
1685 protected MenuItem clustalColour = new MenuItem();
\r
1686 protected MenuItem zappoColour = new MenuItem();
\r
1687 protected MenuItem taylorColour = new MenuItem();
\r
1688 protected MenuItem hydrophobicityColour = new MenuItem();
\r
1689 protected MenuItem helixColour = new MenuItem();
\r
1690 protected MenuItem strandColour = new MenuItem();
\r
1691 protected MenuItem turnColour = new MenuItem();
\r
1692 protected MenuItem buriedColour = new MenuItem();
\r
1693 protected MenuItem userDefinedColour = new MenuItem();
\r
1694 protected MenuItem PIDColour = new MenuItem();
\r
1695 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
1696 MenuItem njTreeBlosumMenuItem = new MenuItem();
\r
1697 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
\r
1698 protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
\r
1699 protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
\r
1700 MenuItem overviewMenuItem = new MenuItem();
\r
1701 protected MenuItem undoMenuItem = new MenuItem();
\r
1702 protected MenuItem redoMenuItem = new MenuItem();
\r
1703 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
1704 MenuItem noColourmenuItem = new MenuItem();
\r
1705 protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
\r
1706 protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
\r
1707 MenuItem findMenuItem = new MenuItem();
\r
1708 Menu searchMenu = new Menu();
\r
1709 protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
\r
1710 protected MenuItem nucleotideColour = new MenuItem();
\r
1711 MenuItem deleteGroups = new MenuItem();
\r
1712 MenuItem delete = new MenuItem();
\r
1713 MenuItem copy = new MenuItem();
\r
1714 MenuItem cut = new MenuItem();
\r
1715 Menu pasteMenu = new Menu();
\r
1716 MenuItem pasteNew = new MenuItem();
\r
1717 MenuItem pasteThis = new MenuItem();
\r
1718 protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
\r
1719 protected MenuItem font = new MenuItem();
\r
1720 protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
\r
1721 protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
\r
1722 protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
\r
1723 MenuItem modifyPID = new MenuItem();
\r
1724 MenuItem modifyConservation = new MenuItem();
\r
1725 protected Menu sortByTreeMenu = new Menu();
\r
1726 Menu sort = new Menu();
\r
1727 Menu calculate = new Menu();
\r
1728 MenuItem inputText = new MenuItem();
\r
1729 Menu helpMenu = new Menu();
\r
1730 MenuItem documentation = new MenuItem();
\r
1731 MenuItem about = new MenuItem();
\r
1732 protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
\r
1733 Panel embeddedMenu;
\r
1734 Label embeddedEdit;
\r
1735 Label embeddedSearch;
\r
1736 Label embeddedView;
\r
1737 Label embeddedColour;
\r
1738 Label embeddedFile;
\r
1739 Label embeddedHelp;
\r
1740 Label embeddedCalculate;
\r
1741 FlowLayout flowLayout1;
\r
1743 private void jbInit() throws Exception {
\r
1745 setMenuBar(alignFrameMenuBar);
\r
1749 // dynamically fill save as menu with available formats
\r
1750 for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)
\r
1753 item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
\r
1756 item.addActionListener(new java.awt.event.ActionListener()
\r
1758 public void actionPerformed(ActionEvent e)
\r
1760 outputText_actionPerformed(e);
\r
1764 outputTextboxMenu.add(item);
\r
1767 fileMenu.setLabel("File");
\r
1768 closeMenuItem.setLabel("Close");
\r
1769 closeMenuItem.addActionListener(this);
\r
1770 editMenu.setLabel("Edit");
\r
1771 viewMenu.setLabel("View");
\r
1772 colourMenu.setLabel("Colour");
\r
1773 calculateMenu.setLabel("Calculate");
\r
1774 selectAllSequenceMenuItem.setLabel("Select all");
\r
1775 selectAllSequenceMenuItem.addActionListener(this);
\r
1776 deselectAllSequenceMenuItem.setLabel("Deselect All");
\r
1777 deselectAllSequenceMenuItem.addActionListener(this);
\r
1778 invertSequenceMenuItem.setLabel("Invert Selection");
\r
1779 invertSequenceMenuItem.addActionListener(this);
\r
1780 remove2LeftMenuItem.setLabel("Remove Left");
\r
1781 remove2LeftMenuItem.addActionListener(this);
\r
1782 remove2RightMenuItem.setLabel("Remove Right");
\r
1783 remove2RightMenuItem.addActionListener(this);
\r
1784 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
\r
1785 removeGappedColumnMenuItem.addActionListener(this);
\r
1786 removeAllGapsMenuItem.setLabel("Remove All Gaps");
\r
1787 removeAllGapsMenuItem.addActionListener(this);
\r
1788 viewBoxesMenuItem.setLabel("Boxes");
\r
1789 viewBoxesMenuItem.setState(true);
\r
1790 viewBoxesMenuItem.addItemListener(this);
\r
1791 viewTextMenuItem.setLabel("Text");
\r
1792 viewTextMenuItem.setState(true);
\r
1793 viewTextMenuItem.addItemListener(this);
\r
1794 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
\r
1795 sortPairwiseMenuItem.addActionListener(this);
\r
1796 sortIDMenuItem.setLabel("by ID");
\r
1797 sortIDMenuItem.addActionListener(this);
\r
1798 sortGroupMenuItem.setLabel("by Group");
\r
1799 sortGroupMenuItem.addActionListener(this);
\r
1800 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
\r
1801 removeRedundancyMenuItem.addActionListener(this);
\r
1802 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
\r
1803 pairwiseAlignmentMenuItem.addActionListener(this);
\r
1804 PCAMenuItem.setLabel("Principal Component Analysis");
\r
1805 PCAMenuItem.addActionListener(this);
\r
1806 averageDistanceTreeMenuItem.setLabel(
\r
1807 "Average Distance Using % Identity");
\r
1808 averageDistanceTreeMenuItem.addActionListener(this);
\r
1809 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
\r
1810 neighbourTreeMenuItem.addActionListener(this);
\r
1811 alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1812 statusBar.setBackground(Color.white);
\r
1813 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
\r
1814 statusBar.setText("Status bar");
\r
1815 outputTextboxMenu.setLabel("Output to Textbox");
\r
1816 clustalColour.setLabel("Clustalx");
\r
1818 clustalColour.addActionListener(this);
\r
1819 zappoColour.setLabel("Zappo");
\r
1820 zappoColour.addActionListener(this);
\r
1821 taylorColour.setLabel("Taylor");
\r
1822 taylorColour.addActionListener(this);
\r
1823 hydrophobicityColour.setLabel("Hydrophobicity");
\r
1824 hydrophobicityColour.addActionListener(this);
\r
1825 helixColour.setLabel("Helix Propensity");
\r
1826 helixColour.addActionListener(this);
\r
1827 strandColour.setLabel("Strand Propensity");
\r
1828 strandColour.addActionListener(this);
\r
1829 turnColour.setLabel("Turn Propensity");
\r
1830 turnColour.addActionListener(this);
\r
1831 buriedColour.setLabel("Buried Index");
\r
1832 buriedColour.addActionListener(this);
\r
1833 userDefinedColour.setLabel("User Defined...");
\r
1834 userDefinedColour.addActionListener(this);
\r
1835 PIDColour.setLabel("Percentage Identity");
\r
1836 PIDColour.addActionListener(this);
\r
1837 BLOSUM62Colour.setLabel("BLOSUM62 Score");
\r
1838 BLOSUM62Colour.addActionListener(this);
\r
1839 avDistanceTreeBlosumMenuItem.setLabel(
\r
1840 "Average Distance Using BLOSUM62");
\r
1841 avDistanceTreeBlosumMenuItem.addActionListener(this);
\r
1842 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
\r
1843 njTreeBlosumMenuItem.addActionListener(this);
\r
1844 annotationPanelMenuItem.setLabel("Show Annotations");
\r
1845 annotationPanelMenuItem.addItemListener(this);
\r
1846 colourTextMenuItem.setLabel("Colour Text");
\r
1847 colourTextMenuItem.addItemListener(this);
\r
1848 overviewMenuItem.setLabel("Overview Window");
\r
1849 overviewMenuItem.addActionListener(this);
\r
1850 undoMenuItem.setEnabled(false);
\r
1851 undoMenuItem.setLabel("Undo");
\r
1852 undoMenuItem.addActionListener(this);
\r
1853 redoMenuItem.setEnabled(false);
\r
1854 redoMenuItem.setLabel("Redo");
\r
1855 redoMenuItem.addActionListener(this);
\r
1856 conservationMenuItem.setLabel("by Conservation");
\r
1857 conservationMenuItem.addItemListener(this);
\r
1858 noColourmenuItem.setLabel("None");
\r
1859 noColourmenuItem.addActionListener(this);
\r
1860 wrapMenuItem.setLabel("Wrap");
\r
1861 wrapMenuItem.addItemListener(this);
\r
1862 renderGapsMenuItem.setLabel("Show Gaps");
\r
1863 renderGapsMenuItem.setState(true);
\r
1864 renderGapsMenuItem.addItemListener(this);
\r
1865 findMenuItem.setLabel("Find...");
\r
1866 findMenuItem.addActionListener(this);
\r
1867 searchMenu.setLabel("Search");
\r
1869 abovePIDThreshold.setLabel("Above Identity Threshold");
\r
1870 abovePIDThreshold.addItemListener(this);
\r
1871 nucleotideColour.setLabel("Nucleotide");
\r
1872 nucleotideColour.addActionListener(this);
\r
1873 deleteGroups.setLabel("Undefine Groups");
\r
1874 deleteGroups.addActionListener(this);
\r
1875 copy.setLabel("Copy");
\r
1876 copy.addActionListener(this);
\r
1877 cut.setLabel("Cut");
\r
1878 cut.addActionListener(this);
\r
1879 delete.setLabel("Delete");
\r
1880 delete.addActionListener(this);
\r
1881 pasteMenu.setLabel("Paste");
\r
1882 pasteNew.setLabel("To New Alignment");
\r
1883 pasteNew.addActionListener(this);
\r
1884 pasteThis.setLabel("Add To This Alignment");
\r
1885 pasteThis.addActionListener(this);
\r
1886 applyToAllGroups.setLabel("Apply Colour To All Groups");
\r
1887 applyToAllGroups.setState(true);
\r
1888 applyToAllGroups.addItemListener(this);
\r
1889 font.setLabel("Font...");
\r
1890 font.addActionListener(this);
\r
1891 scaleAbove.setLabel("Scale Above");
\r
1892 scaleAbove.setState(true);
\r
1893 scaleAbove.setEnabled(false);
\r
1894 scaleAbove.addItemListener(this);
\r
1895 scaleLeft.setEnabled(false);
\r
1896 scaleLeft.setState(true);
\r
1897 scaleLeft.setLabel("Scale Left");
\r
1898 scaleLeft.addItemListener(this);
\r
1899 scaleRight.setEnabled(false);
\r
1900 scaleRight.setState(true);
\r
1901 scaleRight.setLabel("Scale Right");
\r
1902 scaleRight.addItemListener(this);
\r
1903 modifyPID.setLabel("Modify Identity Threshold...");
\r
1904 modifyPID.addActionListener(this);
\r
1905 modifyConservation.setLabel("Modify Conservation Threshold...");
\r
1906 modifyConservation.addActionListener(this);
\r
1907 sortByTreeMenu.setLabel("By Tree Order");
\r
1908 sort.setLabel("Sort");
\r
1909 calculate.setLabel("Calculate Tree");
\r
1910 inputText.setLabel("Input from textbox");
\r
1911 inputText.addActionListener(this);
\r
1913 helpMenu.setLabel("Help");
\r
1914 documentation.setLabel("Documentation");
\r
1915 documentation.addActionListener(this);
\r
1917 about.setLabel("About...");
\r
1918 about.addActionListener(this);
\r
1919 seqLimits.setState(true);
\r
1920 seqLimits.setLabel("Show Sequence Limits");
\r
1921 seqLimits.addItemListener(this);
\r
1922 featureSettings.setLabel("Feature Settings...");
\r
1923 featureSettings.addActionListener(this);
\r
1924 sequenceFeatures.setLabel("Sequence Features");
\r
1925 sequenceFeatures.addItemListener(this);
\r
1926 sequenceFeatures.setState(true);
\r
1928 alignFrameMenuBar.add(fileMenu);
\r
1929 alignFrameMenuBar.add(editMenu);
\r
1930 alignFrameMenuBar.add(searchMenu);
\r
1931 alignFrameMenuBar.add(viewMenu);
\r
1932 alignFrameMenuBar.add(colourMenu);
\r
1933 alignFrameMenuBar.add(calculateMenu);
\r
1934 alignFrameMenuBar.add(helpMenu);
\r
1935 fileMenu.add(inputText);
\r
1936 fileMenu.add(outputTextboxMenu);
\r
1937 fileMenu.addSeparator();
\r
1938 fileMenu.add(closeMenuItem);
\r
1939 editMenu.add(undoMenuItem);
\r
1940 editMenu.add(redoMenuItem);
\r
1941 editMenu.add(cut);
\r
1942 editMenu.add(copy);
\r
1943 editMenu.add(pasteMenu);
\r
1944 editMenu.add(delete);
\r
1945 editMenu.addSeparator();
\r
1946 editMenu.add(selectAllSequenceMenuItem);
\r
1947 editMenu.add(deselectAllSequenceMenuItem);
\r
1948 editMenu.add(invertSequenceMenuItem);
\r
1949 editMenu.add(deleteGroups);
\r
1950 editMenu.addSeparator();
\r
1951 editMenu.add(remove2LeftMenuItem);
\r
1952 editMenu.add(remove2RightMenuItem);
\r
1953 editMenu.add(removeGappedColumnMenuItem);
\r
1954 editMenu.add(removeAllGapsMenuItem);
\r
1955 editMenu.add(removeRedundancyMenuItem);
\r
1956 searchMenu.add(findMenuItem);
\r
1957 viewMenu.add(font);
\r
1958 viewMenu.addSeparator();
\r
1959 viewMenu.add(seqLimits);
\r
1960 viewMenu.addSeparator();
\r
1961 viewMenu.add(wrapMenuItem);
\r
1962 viewMenu.add(scaleAbove);
\r
1963 viewMenu.add(scaleLeft);
\r
1964 viewMenu.add(scaleRight);
\r
1965 viewMenu.addSeparator();
\r
1966 viewMenu.add(viewBoxesMenuItem);
\r
1967 viewMenu.add(viewTextMenuItem);
\r
1968 viewMenu.add(colourTextMenuItem);
\r
1969 viewMenu.add(renderGapsMenuItem);
\r
1970 viewMenu.add(annotationPanelMenuItem);
\r
1971 viewMenu.addSeparator();
\r
1972 viewMenu.add(overviewMenuItem);
\r
1973 colourMenu.add(applyToAllGroups);
\r
1974 colourMenu.addSeparator();
\r
1975 colourMenu.add(noColourmenuItem);
\r
1976 colourMenu.add(clustalColour);
\r
1977 colourMenu.add(BLOSUM62Colour);
\r
1978 colourMenu.add(PIDColour);
\r
1979 colourMenu.add(zappoColour);
\r
1980 colourMenu.add(taylorColour);
\r
1981 colourMenu.add(hydrophobicityColour);
\r
1982 colourMenu.add(helixColour);
\r
1983 colourMenu.add(strandColour);
\r
1984 colourMenu.add(turnColour);
\r
1985 colourMenu.add(buriedColour);
\r
1986 colourMenu.add(nucleotideColour);
\r
1987 colourMenu.add(userDefinedColour);
\r
1988 colourMenu.addSeparator();
\r
1989 colourMenu.add(conservationMenuItem);
\r
1990 colourMenu.add(modifyConservation);
\r
1991 colourMenu.add(abovePIDThreshold);
\r
1992 colourMenu.add(modifyPID);
\r
1993 calculateMenu.add(sort);
\r
1994 calculateMenu.add(calculate);
\r
1995 calculateMenu.addSeparator();
\r
1996 calculateMenu.add(pairwiseAlignmentMenuItem);
\r
1997 calculateMenu.add(PCAMenuItem);
\r
1998 this.add(statusBar, BorderLayout.SOUTH);
\r
1999 pasteMenu.add(pasteNew);
\r
2000 pasteMenu.add(pasteThis);
\r
2001 sort.add(sortIDMenuItem);
\r
2002 sort.add(sortByTreeMenu);
\r
2003 sort.add(sortGroupMenuItem);
\r
2004 sort.add(sortPairwiseMenuItem);
\r
2005 calculate.add(averageDistanceTreeMenuItem);
\r
2006 calculate.add(neighbourTreeMenuItem);
\r
2007 calculate.add(avDistanceTreeBlosumMenuItem);
\r
2008 calculate.add(njTreeBlosumMenuItem);
\r
2009 helpMenu.add(documentation);
\r
2010 helpMenu.add(about);
\r
2013 public void setEmbedded()
\r
2016 embeddedMenu = new Panel();
\r
2017 embeddedEdit = new Label();
\r
2018 embeddedSearch = new Label();
\r
2019 embeddedView = new Label();
\r
2020 embeddedColour = new Label();
\r
2021 embeddedFile = new Label();
\r
2022 embeddedHelp = new Label();
\r
2023 embeddedCalculate = new Label();
\r
2024 flowLayout1 = new FlowLayout();
\r
2025 embeddedMenu.setBackground(Color.lightGray);
\r
2026 embeddedMenu.setLayout(flowLayout1);
\r
2027 embeddedEdit.setText("Edit");
\r
2028 embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2029 embeddedSearch.setText("Search");
\r
2030 embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2031 embeddedView.setText("View");
\r
2032 embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2033 embeddedColour.setText("Colour");
\r
2034 embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2035 embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2036 embeddedFile.setText("File");
\r
2037 embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2038 embeddedHelp.setText("Help");
\r
2039 embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
\r
2040 embeddedCalculate.setText("Calculate");
\r
2041 embeddedMenu.add(embeddedFile);
\r
2042 embeddedMenu.add(embeddedEdit);
\r
2043 embeddedMenu.add(embeddedSearch);
\r
2044 embeddedMenu.add(embeddedView);
\r
2045 embeddedMenu.add(embeddedColour);
\r
2046 embeddedMenu.add(embeddedCalculate);
\r
2047 embeddedMenu.add(embeddedHelp);
\r
2048 flowLayout1.setAlignment(FlowLayout.LEFT);
\r
2049 flowLayout1.setHgap(2);
\r
2050 flowLayout1.setVgap(0);
\r
2051 embeddedFile.addMouseListener(this);
\r
2052 embeddedEdit.addMouseListener(this);
\r
2053 embeddedSearch.addMouseListener(this);
\r
2054 embeddedView.addMouseListener(this);
\r
2055 embeddedColour.addMouseListener(this);
\r
2056 embeddedCalculate.addMouseListener(this);
\r
2057 embeddedHelp.addMouseListener(this);
\r
2059 setVisible(false);
\r
2060 fileMenu.remove(closeMenuItem);
\r
2061 fileMenu.remove(2); // Seperator
\r
2063 applet.setLayout(new BorderLayout());
\r
2064 applet.add(embeddedMenu, BorderLayout.NORTH);
\r
2065 applet.add(statusBar, BorderLayout.SOUTH);
\r
2066 applet.validate();
\r
2069 alignPanel.setSize(applet.size().width, applet.size().height
\r
2070 - embeddedMenu.HEIGHT - statusBar.HEIGHT);
\r
2072 applet.add(alignPanel, BorderLayout.CENTER);
\r
2073 applet.validate();
\r
2078 PopupMenu filePopup, editPopup, searchPopup,
\r
2079 viewPopup, colourPopup, calculatePopup, helpPopup;
\r
2080 MenuItem featureSettings = new MenuItem();
\r
2081 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
\r
2083 public void mousePressed(MouseEvent evt)
\r
2085 PopupMenu popup = null;
\r
2086 Label source = (Label)evt.getSource();
\r
2087 if(source==embeddedFile)
\r
2089 popup = filePopup = genPopupMenu(filePopup, fileMenu);
\r
2091 else if(source==embeddedEdit)
\r
2093 popup = editPopup = genPopupMenu(editPopup, editMenu);
\r
2095 else if(source==embeddedSearch)
\r
2097 popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
\r
2099 else if(source==embeddedView)
\r
2101 popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
\r
2103 else if(source==embeddedColour)
\r
2105 popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
\r
2107 else if(source==embeddedCalculate)
\r
2109 popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
\r
2111 else if(source==embeddedHelp)
\r
2113 popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
\r
2116 embeddedMenu.add(popup);
\r
2117 popup.show(embeddedMenu,
\r
2118 source.getBounds().x,
\r
2119 source.getBounds().y + source.getBounds().getSize().height);
\r
2122 PopupMenu genPopupMenu(PopupMenu popup, Menu original)
\r
2128 popup = new PopupMenu();
\r
2129 int m, mSize = original.getItemCount();
\r
2130 for(m=0; m<mSize; m++)
\r
2132 popup.add(original.getItem(m));
\r
2139 public void mouseClicked(MouseEvent evt)
\r
2141 public void mouseReleased(MouseEvent evt)
\r
2143 public void mouseEntered(MouseEvent evt)
\r
2145 public void mouseExited(MouseEvent evt)
\r